ngsplot: lib/coverage.r annotate

annotate lib/coverage.r @ 0:3ca58369469c draft

planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n'

author	artbio
date	Wed, 06 Dec 2017 19:01:53 -0500
parents
children

rev	line source
0 3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	1 # Function to check if the range exceeds coverage vector boundaries.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	2 checkBound <- function(start, end, range, chrlen){
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	3 if(end + range > chrlen \|\| start - range < 1)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	4 return(FALSE) # out of boundary.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	5 else
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	6 return(TRUE)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	7 }
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	8
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	9 Bin <- function(v, n) {
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	10 # Function to bin a coverage vector.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	11 # Args:
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	12 # v: coverage vector.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	13 # n: number of bins.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	14 # Return: vector of binned values.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	15
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	16 bin.bound <- seq(1, length(v), length.out=n + 1)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	17 sapply(1:n, function(i) {
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	18 mean(v[bin.bound[i]:bin.bound[i + 1]])
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	19 })
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	20 }
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	21
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	22 SplineRev3Sec <- function(cov.list, v.fls, pts.list, v.strand, algo="spline") {
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	23 # For 3 sections of continuous coverage, spline each according to specified
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	24 # data points and return concatenated, interpolated curves.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	25 # Args:
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	26 # cov.list: a list of coverage vectors. Each vector represents a gene.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	27 # v.fls: vector of flanking region size.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	28 # pts.list: a list of three integers for data points.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	29 # v.strand: factor vector of strands.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	30 # algo: algorithm used to normalize coverage vectors (spline, bin).
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	31 # Return: matrix of interpolated coverage: each row represents a gene; each
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	32 # column represents a data point. Coverage from exons are concatenated.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	33 # Notes: the names of cov.list and pts.list must be the same for index purpose.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	34 # Suggested: use 'l', 'm', and 'r' for the names.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	35
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	36 # Create an empty coveage matrix first.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	37 tot.pts <- sum(unlist(pts.list)) - 2
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	38 cov.mat <- matrix(nrow=length(cov.list), ncol=tot.pts)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	39
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	40 for(i in 1:length(cov.list)) {
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	41 left.cov <- head(cov.list[[i]], n=v.fls[i])
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	42 right.cov <- tail(cov.list[[i]], n=v.fls[i])
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	43 mid.cov <- window(cov.list[[i]], start=v.fls[i] + 1,
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	44 width=length(cov.list[[i]]) - 2*v.fls[i])
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	45 if(algo == "spline") {
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	46 left.cov <- spline(1:length(left.cov), left.cov, n=pts.list$l)$y
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	47 right.cov <- spline(1:length(right.cov), right.cov, n=pts.list$r)$y
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	48 mid.cov <- spline(1:length(mid.cov), mid.cov, n=pts.list$m)$y
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	49 } else if(algo == "bin") {
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	50 left.cov <- Bin(left.cov, n=pts.list$l)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	51 right.cov <- Bin(right.cov, n=pts.list$r)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	52 mid.cov <- Bin(mid.cov, n=pts.list$m)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	53 } else {
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	54 # pass.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	55 }
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	56 # Fuse the two points at the boundary and concatenate.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	57 f1 <- (tail(left.cov, n=1) + head(mid.cov, n=1)) / 2
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	58 f2 <- (tail(mid.cov, n=1) + head(right.cov, n=1)) / 2
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	59 con.cov <- c(left.cov[-length(left.cov)], f1,
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	60 mid.cov[-c(1, length(mid.cov))],
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	61 f2, right.cov[-1])
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	62 # browser()
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	63 if(v.strand[i] == '+') {
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	64 cov.mat[i, ] <- con.cov
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	65 } else {
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	66 cov.mat[i, ] <- rev(con.cov)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	67 }
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	68 }
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	69
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	70 cov.mat
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	71 }
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	72
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	73 extrCov3Sec <- function(v.chrom, v.start, v.end, v.fls, v.strand, m.pts, f.pts,
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	74 bufsize, algo, ...) {
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	75 # Extract and interpolate coverage vectors from genomic regions with 3 sections.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	76 # Args:
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	77 # v.chrom: factor vector of chromosome names.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	78 # v.start: integer vector of region start.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	79 # v.end: integer vector of region end.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	80 # v.fls: integer vector of flanking region size in bps.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	81 # v.strand: factor vector of gene strands.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	82 # m.pts: data points for middle interval.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	83 # f.pts: data points for flanking region.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	84 # bufsize: integer; buffers are added to both ends of each region.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	85 # algo: algorithm used to normalize coverage vectors.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	86 # Return: matrix of interpolated coverage: each row represents a gene; each
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	87 # column represents a data point.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	88
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	89 interflank.gr <- GRanges(seqnames=v.chrom, ranges=IRanges(
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	90 start=v.start - v.fls - bufsize,
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	91 end=v.end + v.fls + bufsize))
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	92 interflank.cov <- covBamExons(interflank.gr, v.strand, ...)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	93
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	94 # Trim buffers from coverage vectors.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	95 interflank.cov <- lapply(interflank.cov, function(v) {
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	96 window(v, start=bufsize + 1, width=length(v) - 2 * bufsize)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	97 })
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	98
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	99 # Interpolate and reverse coverage vectors.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	100 SplineRev3Sec(interflank.cov, v.fls, list(l=f.pts, m=m.pts, r=f.pts),
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	101 v.strand, algo)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	102 }
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	103
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	104 sub3CovList <- function(all.cov, v.left, v.right) {
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	105 # For a list of coverage vectors, separate them into three lists.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	106 # Args:
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	107 # all.cov: list of coverage vectors.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	108 # v.left: integer vector of left flanking size.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	109 # v.right: integer vector of right flanking size.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	110 # Return: list of lists of coverage vectors. The outer list is named as:
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	111 # "l", "m", "r".
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	112
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	113 left.cov <- foreach(i=icount(length(all.cov))) %do% {
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	114 head(all.cov[[i]], n=v.left[i])
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	115 }
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	116 mid.cov <- foreach(i=icount(length(all.cov))) %do% {
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	117 len <- length(all.cov[[i]])
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	118 all.cov[[i]][ (v.left[i] + 1) : (len - v.right[i]) ]
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	119 }
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	120 right.cov <- foreach(i=icount(length(all.cov))) %do% {
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	121 tail(all.cov[[i]], n=v.right[i])
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	122 }
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	123 list(l=left.cov, m=mid.cov, r=right.cov)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	124 }
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	125
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	126 extrCovExons <- function(v.chrom, exonranges.list, v.fls, v.strand,
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	127 m.pts, f.pts, bufsize, algo, ...) {
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	128 # Extract coverage vectors for transcripts with exon models.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	129 # Args:
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	130 # v.chrom: factor vector of chromosome names.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	131 # exonranges.list: list of IRanges objects for exon coordinates.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	132 # v.fls: integer vector of flanking region size in bps.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	133 # v.strand: factor vector of gene strands.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	134 # m.pts: data points for middle interval.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	135 # f.pts: data points for flanking region.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	136 # bufsize: integer; buffers are added to both ends of each region.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	137 # algo: algorithm used to normalize coverage vectors.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	138 # Return: matrix of interpolated coverage: each row represents a gene; each
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	139 # column represents a data point. Coverage from exons are concatenated.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	140
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	141 # Construct ranges including exon and flanking regions.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	142 exonflank.list <- vector('list', length=length(exonranges.list))
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	143 for(i in 1:length(exonranges.list)) {
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	144 r.mod <- exonranges.list[[i]] # IRanges object to be modified.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	145 n <- length(r.mod)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	146 # Add flanking and buffer regions.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	147 start(r.mod)[1] <- start(r.mod)[1] - v.fls[i] - bufsize
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	148 end(r.mod)[n] <- end(r.mod)[n] + v.fls[i] + bufsize
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	149 exonflank.list[[i]] <- GRanges(seqnames=v.chrom[i], ranges=r.mod)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	150 }
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	151
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	152 exonflank.cov <- covBamExons(exonflank.list, v.strand, ...)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	153
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	154 # Trim buffers from coverage vectors.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	155 exonflank.cov <- lapply(exonflank.cov, function(v) {
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	156 window(v, start=bufsize + 1, width=length(v) - 2 * bufsize)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	157 })
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	158
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	159 SplineRev3Sec(exonflank.cov, v.fls, list(l=f.pts, m=m.pts, r=f.pts),
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	160 v.strand, algo)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	161 }
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	162
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	163
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	164 extrCovMidp <- function(v.chrom, v.midp, flanksize, v.strand, pts, bufsize,
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	165 algo, ...) {
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	166 # Extract coverage vectors with a middle point and symmetric flanking regions.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	167 # Args:
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	168 # v.chrom: factor vector of chromosome names.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	169 # v.midp: integer vector of middle points.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	170 # flanksize: integer of flanking region size in bps.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	171 # v.strand: factor vector of gene strands.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	172 # pts: data points to spline into.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	173 # bufsize: integer; buffers are added to both ends of each region.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	174 # algo: algorithm used to normalize coverage vectors.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	175 # Return: matrix of interpolated coverage: each row represents a gene; each
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	176 # column represents a data point.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	177
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	178 granges <- GRanges(seqnames=v.chrom, ranges=IRanges(
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	179 start=v.midp - flanksize - bufsize,
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	180 end=v.midp + flanksize + bufsize))
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	181 cov.list <- covBamExons(granges, v.strand, ...)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	182
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	183 # Trim buffers from coverage vectors.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	184 cov.list <- lapply(cov.list, function(v) {
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	185 window(v, start=bufsize + 1, width=length(v) - 2 * bufsize)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	186 })
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	187
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	188 # Interpolate and reverse coverage vectors and assemble into a matrix.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	189 cov.mat <- matrix(nrow=length(cov.list), ncol=pts)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	190 for(i in 1:length(cov.list)) {
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	191 if(is.null(cov.list[[i]])) {
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	192 cov.mat[i, ] <- vector('integer', length=pts)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	193 } else {
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	194 if(algo == "spline") {
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	195 cov.mat[i, ] <- spline(1:length(cov.list[[i]]), cov.list[[i]],
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	196 n=pts)$y
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	197 } else if(algo == "bin") {
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	198 cov.mat[i, ] <- Bin(cov.list[[i]], n=pts)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	199 } else {
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	200 # pass.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	201 }
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	202 if(v.strand[i] == '-') {
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	203 cov.mat[i, ] <- rev(cov.mat[i, ])
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	204 }
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	205 }
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	206 }
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	207 cov.mat
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	208 }
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	209
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	210 scanBamRevOrder <- function(org.gr, sbp) {
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	211 # ScanBamParam re-arranges the input genomic ranges. Use range info to
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	212 # construct a string vector to find the order to reverse it.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	213 org.grnames <- with(org.gr, paste(seqnames, start, end, sep=':'))
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	214 sbw.gr <- as.data.frame(bamWhich(sbp)) # scan-bam-ed
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	215 if('space' %in% names(sbw.gr)) {
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	216 sbw.grnames <- with(sbw.gr, paste(space, start, end, sep=':'))
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	217 } else if('group_name' %in% names(sbw.gr)) {
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	218 sbw.grnames <- with(sbw.gr, paste(group_name, start, end, sep=':'))
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	219 } else {
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	220 stop("Cannot locate chromosome names in extracted short reads. Report
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	221 this problem using issue tracking or discussion forum.\n")
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	222 }
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	223
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	224 match(org.grnames, sbw.grnames)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	225 }
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	226
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	227 genZeroList <- function(llen, v.vlen) {
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	228 # Generate a list of specific length with each element being an Rle vector of
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	229 # zeros with specific length.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	230 # Args:
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	231 # llen: list length
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	232 # v.vlen: vector of vector lengths.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	233
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	234 llen <- as.integer(llen)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	235 stopifnot(llen > 0)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	236 res <- vector('list', length=llen)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	237 for(i in 1:llen) {
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	238 res[[i]] <- Rle(0, v.vlen[i])
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	239 }
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	240 res
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	241 }
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	242
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	243 covBamExons <- function(granges.dat, v.strand, bam.file, sn.inbam, fraglen,
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	244 map.qual=20, bowtie=F,
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	245 strand.spec=c('both', 'same', 'opposite')) {
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	246 # Extract coverage vectors from bam file for a list of transcripts of multiple
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	247 # exons.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	248 # Args:
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	249 # granges.dat: a GRanges object representing a set of genomic ranges or a
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	250 # list of GRanges objects each representing a set of exonic
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	251 # ranges.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	252 # v.strand: vector of strand info.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	253 # bam.file: character string refers to the path of a bam file.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	254 # sn.inbam: vector of chromosome names in the bam file.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	255 # fraglen: fragment length.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	256 # map.qual: mapping quality to filter reads.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	257 # bowtie: boolean to indicate whether the aligner was Bowtie-like or not.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	258 # strand.spec: string desc. for strand-specific coverage calculation.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	259 # Return: list of coverage vectors, each vector represents a transcript.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	260
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	261 strand.spec <- match.arg(strand.spec)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	262
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	263 if(class(granges.dat) == 'list') {
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	264 # Construct a GRanges object representing DNA sequences.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	265 v.seqnames <- sapply(granges.dat,
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	266 function(x) as.character(seqnames(x)[1]))
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	267 v.start <- sapply(granges.dat, function(x) start(ranges(x))[1])
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	268 v.end <- sapply(granges.dat, function(x) tail(end(ranges(x)), n=1))
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	269 granges.dna <- GRanges(seqnames=v.seqnames,
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	270 ranges=IRanges(start=v.start, end=v.end))
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	271 # Obtain mRNA(including flanking) length for each gene.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	272 repr.lens <- sapply(granges.dat, function(g) {
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	273 sum(end(g) - start(g) + 1)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	274 })
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	275 } else {
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	276 v.seqnames <- as.character(seqnames(granges.dat))
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	277 v.start <- start(granges.dat)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	278 v.end <- end(granges.dat)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	279 granges.dna <- granges.dat
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	280 repr.lens <- v.end - v.start + 1
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	281 granges.dat <- vector('list', length(granges.dna)) # set null tags.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	282 }
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	283
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	284 # Filter transcripts whose chromosomes do not match bam file.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	285 inbam.mask <- as.character(seqnames(granges.dna)) %in% sn.inbam
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	286 if(!any(inbam.mask)) { # none matches.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	287 return(genZeroList(length(granges.dna), repr.lens))
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	288 }
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	289
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	290 # scanBamWhat: the info that need to be extracted from a bam file.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	291 sbw <- c('pos', 'qwidth', 'mapq', 'strand', 'rname',
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	292 'mrnm', 'mpos', 'isize')
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	293 sbp <- ScanBamParam(what=sbw, which=granges.dna[inbam.mask],
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	294 flag=scanBamFlag(isUnmappedQuery=F,
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	295 isNotPassingQualityControls=F,
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	296 isDuplicate=F))
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	297
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	298 # Scan bam file to retrieve short reads.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	299 sr.in.ranges <- tryCatch(scanBam(bam.file, param=sbp), error=function(e) e)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	300 if(class(sr.in.ranges)[1] == 'simpleError') {
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	301 # This is not supposed to happen after those unmatched seqnames are
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	302 # removed. I keep it for safty.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	303 return(genZeroList(length(granges.dna), repr.lens))
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	304 }
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	305
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	306 # Restore the original order.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	307 sr.in.ranges <- sr.in.ranges[scanBamRevOrder(
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	308 as.data.frame(granges.dna[inbam.mask]), sbp)]
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	309
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	310 CalcReadsCov <- function(srg, start, end, gr.rna, repr.len, strand) {
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	311 # Calculate short read coverage for each gene/region.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	312 # Args:
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	313 # srg: extracted short reads in gene.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	314 # start: start position of the DNA sequence.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	315 # end: end position of the DNA sequence.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	316 # gr.rna: GRanges object (multiple ranges) representing exon sequences.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	317 # This can be NULL indicating the input ranges are DNAs.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	318 # repr.len: DNA or mRNA sequence length.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	319 # strand: transcript strand (+/-).
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	320 # Returns: a coverage vector for the gene.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	321
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	322 # browser()
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	323 # Special handling for bowtie mapping.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	324 if(bowtie) {
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	325 srg <- within(srg, mapq[is.na(mapq)] <- 254) # within!
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	326 }
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	327 # Filter short reads by mapping quality.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	328 all.mask <- srg$mapq >= map.qual
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	329
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	330 # Subset by strand info.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	331 if(strand.spec != 'both') {
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	332 if(strand.spec == 'same') {
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	333 s.mask <- srg$strand == as.character(strand)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	334 } else {
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	335 s.mask <- srg$strand != as.character(strand)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	336 }
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	337 all.mask <- all.mask & s.mask
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	338 }
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	339
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	340 # If paired, filter reads that are not properly paired.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	341 paired <- all(with(srg, is.na(isize) \| isize != 0))
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	342 if(paired) {
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	343 p.mask <- with(srg, rname == mrnm & xor(strand == '+', isize < 0))
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	344 all.mask <- all.mask & p.mask
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	345 }
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	346
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	347 # Apply all the filters on short reads.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	348 srg <- lapply(srg, `[`, which(all.mask))
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	349
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	350 # Calculate coverage.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	351 if(length(srg[[1]]) > 0) {
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	352 if(paired) {
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	353 cov.pos <- with(srg, ifelse(isize < 0, mpos, pos))
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	354 cov.wd <- abs(srg$isize)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	355 } else {
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	356 # Adjust negative read positions for physical coverage.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	357 cov.pos <- with(srg, ifelse(strand == '-',
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	358 pos - fraglen + qwidth, pos))
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	359 cov.wd <- fraglen
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	360 }
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	361 # Shift reads by subtracting start positions.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	362 cov.pos <- cov.pos - start + 1
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	363 # Calculate physical coverage on the whole genebody.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	364 covg <- coverage(IRanges(start=cov.pos, width=cov.wd),
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	365 width=end - start + 1, method='sort')
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	366
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	367 if(!is.null(gr.rna)) { # RNA-seq.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	368 # Shift exonic ranges by subtracting start positions.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	369 # BE careful with negative start positions! Need to adjust end
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	370 # positions first(or the GRanges lib will emit errors if
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	371 # start > end).
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	372 # Negative start positions happen when flanking region exceeds
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	373 # the chromosomal start.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	374 if(start > 0) {
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	375 start(gr.rna) <- start(gr.rna) - start + 1
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	376 end(gr.rna) <- end(gr.rna) - start + 1
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	377 } else {
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	378 end(gr.rna) <- end(gr.rna) - start + 1
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	379 start(gr.rna) <- start(gr.rna) - start + 1
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	380 }
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	381 # Concatenate all exon coverages.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	382 covg[ranges(gr.rna)]
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	383 } else { # ChIP-seq.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	384 covg
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	385 }
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	386 } else {
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	387 Rle(0, repr.len)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	388 }
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	389 }
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	390
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	391 covg.allgenes <- mapply(CalcReadsCov, srg=sr.in.ranges,
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	392 start=v.start, end=v.end, gr.rna=granges.dat,
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	393 repr.len=repr.lens, strand=v.strand, SIMPLIFY=F)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	394 }
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	395
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	396 bamFileList <- function(ctg.tbl) {
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	397 # Determine the bam files involved in the configuration and whether it is a
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	398 # bam file pair setup.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	399 # Args:
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	400 # ctg.tbl: coverage-genelist-title table.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	401
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	402 cov.uniq <- unique(ctg.tbl$cov)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	403 cov.list <- strsplit(cov.uniq, ':')
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	404 v.nbam <- sapply(cov.list, length)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	405 v.bbp <- v.nbam == 2
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	406 if(all(v.bbp)) {
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	407 bbp <- T
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	408 } else if(all(!v.bbp)) {
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	409 bbp <- F
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	410 } else {
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	411 stop("No mix of bam and bam-pair allowed in configuration.\n")
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	412 }
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	413
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	414 list(bbp=bbp, bam.list=unique(unlist(cov.list)))
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	415 }
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	416
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	417 estiMapqStyle <- function(bam.file){
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	418 # Estimate the mapping quality style. Return TRUE if it is SAM standard.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	419 # Sample 1000 mapped reads from bam file, and if the mapq of reads
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	420 # over half are NA, then return FALSE, because it is quite possible that
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	421 # the aligner using coding style as bowtie, 255 as highest score.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	422 # Args:
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	423 # bam.file: bam file to be sampled.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	424
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	425 sbw <- c('pos', 'qwidth', 'mapq', 'strand')
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	426 sbp <- ScanBamParam(what=sbw, flag=scanBamFlag(
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	427 isUnmappedQuery=F, isDuplicate=F))
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	428 samp <- BamSampler(bam.file, yieldSize=500)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	429 samp.reads <- scanBam(samp, param=sbp)[[1]]
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	430 samp.len <- length(samp.reads[["mapq"]])
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	431 mapq.255 <- sum(is.na(samp.reads[["mapq"]]))
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	432 if(mapq.255/samp.len >= 0.5){
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	433 return(FALSE)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	434 }else{
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	435 return(TRUE)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	436 }
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	437 }
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	438
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	439 headerIndexBam <- function(bam.list) {
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	440 # Read bam header to determine mapping method.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	441 # Index bam files if not done yet.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	442 # Args:
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	443 # ctg.tbl: coverage-genelist-title table.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	444
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	445 v.map.bowtie <- vector('logical', length=length(bam.list))
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	446 for(i in 1:length(bam.list)) {
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	447 bam.file <- bam.list[i]
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	448
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	449 # Index bam file.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	450 if(!file.exists(paste(bam.file, ".bai", sep=""))) {
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	451 indexBam(bam.file)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	452 }
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	453
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	454 # Derive mapping program.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	455 header <- scanBamHeader(bam.file)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	456 map.prog <- try(strsplit(header[[1]]$text$'@PG'[[1]], ':')[[1]][2],
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	457 silent=T)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	458 if(class(map.prog) != "try-error") {
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	459 map.style <- grepl('tophat\|bowtie\|bedtools\|star', map.prog,
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	460 ignore.case=T)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	461 if(map.style){
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	462 v.map.bowtie[i] <- TRUE
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	463 next
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	464 }
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	465 map.style <- grepl('bwa\|casava\|gem', map.prog, ignore.case=T)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	466 if(map.style) {
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	467 v.map.bowtie[i] <- FALSE
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	468 next
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	469 }
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	470 # if(estiMapqStyle(bam.file)){
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	471 # warning(sprintf("Aligner for: %s cannot be determined. Style of
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	472 # standard SAM mapping score will be used.", bam.file))
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	473 # v.map.bowtie[i] <- FALSE
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	474 # }else{
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	475 # warning(sprintf("Aligner for: %s cannot be determined. Style of
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	476 # Bowtie-like SAM mapping score will be used. Would you mind to tell us what
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	477 # aligner you are using?", bam.file))
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	478 # v.map.bowtie[i] <- TRUE
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	479 # }
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	480 }
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	481 # else {
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	482 # cat("\n")
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	483 # if(estiMapqStyle(bam.file)){
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	484 # warning(sprintf("Aligner for: %s cannot be determined. Style of
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	485 # standard SAM mapping score will be used.", bam.file))
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	486 # v.map.bowtie[i] <- FALSE
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	487 # }else{
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	488 # warning(sprintf("Aligner for: %s cannot be determined. Style of
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	489 # Bowtie-like SAM mapping score will be used.", bam.file))
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	490 # v.map.bowtie[i] <- TRUE
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	491 # }
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	492 # }
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	493 warning(sprintf("Aligner for: %s cannot be determined. Style of
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	494 standard SAM mapping score will be used. Would you mind submitting an issue
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	495 report to us on Github? This will benefit people using the same aligner.",
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	496 bam.file))
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	497 v.map.bowtie[i] <- FALSE
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	498 }
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	499 names(v.map.bowtie) <- bam.list
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	500
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	501 v.map.bowtie
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	502 }
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	503
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	504 libSizeBam <- function(bam.list) {
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	505 # Obtain library sizes by counting qualified bam records.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	506 # Args:
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	507 # ctg.tbl: coverage-genelist-title table.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	508
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	509 # Count only reads that are mapped, primary, passed quality control and
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	510 # un-duplicated.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	511 sbp <- ScanBamParam(flag=scanBamFlag(isUnmappedQuery=F, isSecondaryAlignment=F,
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	512 isNotPassingQualityControls=F, isDuplicate=F))
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	513 v.lib.size <- vector('integer', length=length(bam.list))
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	514 for(i in 1:length(bam.list)) {
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	515 bfn <- bam.list[i] # bam file name.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	516 cfn <- paste(basename(bfn), '.cnt', sep='') # count file name.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	517 if(file.exists(cfn)) {
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	518 v.lib.size[i] <- as.integer(readLines(cfn, n=1))
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	519 } else {
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	520 cnt.bam <- countBam(bfn, param=sbp)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	521 v.lib.size[i] <- cnt.bam$records
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	522 writeLines(as.character(v.lib.size[i]), cfn)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	523 }
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	524 names(v.lib.size)[i] <- bfn
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	525 }
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	526
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	527 v.lib.size
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	528 }
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	529
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	530 seqnamesBam <- function(bam.list) {
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	531 # Obtain chromosome names for each bam file. This list must be used to filter
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	532 # genomic regions before scanBam or it terminates immaturely.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	533 # ctg.tbl: coverage-genelist-title table.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	534
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	535 # browser()
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	536 sn.list <- lapply(scanBamHeader(bam.list), function(h) {
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	537 names(h$targets)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	538 })
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	539 names(sn.list) <- bam.list
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	540
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	541 sn.list
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	542 }
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	543
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	544 chrTag <- function(sn.inbam) {
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	545 # Check whether the chromosome name format in the bam file contains 'chr' or not.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	546 # Args:
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	547 # sn.inbam: seqnames in the bam file.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	548
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	549 n.chr <- length(grep('^chr', sn.inbam))
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	550 if(n.chr == 0) {
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	551 chr.tag <- F
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	552 } else if(n.chr == length(sn.inbam)) {
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	553 chr.tag <- T
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	554 } else {
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	555 return("Inconsistent chromosome names in bam file. Check bam header.")
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	556 }
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	557
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	558 chr.tag
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	559 }
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	560
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	561 chunkIndex <- function(tot.gene, gcs) {
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	562 # Create chunk indices according to total number of genes and chunk size.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	563 # Args:
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	564 # tot.gene: total number of genes.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	565 # gcs: gene chunk size.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	566
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	567 nchk <- ceiling(tot.gene / gcs) # number of chunks.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	568 chkidx.list <- vector('list', length=nchk) # chunk indices list.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	569 chk.start <- 1 # chunk start.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	570 i.chk <- idiv(tot.gene, chunkSize=gcs)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	571 for(i in 1:nchk) {
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	572 chk.size <- nextElem(i.chk)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	573 chkidx.list[[i]] <- c(chk.start, chk.start + chk.size - 1)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	574 chk.start <- chk.start + chk.size
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	575 }
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	576
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	577 chkidx.list
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	578 }
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	579
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	580 covMatrix <- function(debug, chkidx.list, coord, rnaseq.gb, exonmodel, libsize,
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	581 spit.dot=T, ...) {
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	582 # Function to generate a coverage matrix for all genes.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	583 # Args:
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	584 # debug: boolean tag for debugging.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	585 # chkidx.list: list of (start, end) indices for each chunk.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	586 # coord: dataframe of gene coordinates.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	587 # rnaseq.gb: boolean for RNA-seq genebody plot.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	588 # exonmodel: exon model data object.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	589 # libsize: total read count for this bam file.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	590 # spit.dot: boolean to control sptting '.' to consoles.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	591 # Return: normalized coverage matrix for all genes, each row represents a gene.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	592
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	593
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	594 if(!debug) {
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	595 # Extract coverage and combine into a matrix.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	596 result.matrix <- foreach(chk=chkidx.list, .combine='rbind',
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	597 .multicombine=T) %dopar% {
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	598 if(spit.dot) {
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	599 cat(".")
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	600 }
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	601 i <- chk[1]:chk[2] # chunk: start -> end
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	602 # If RNA-seq, retrieve exon ranges.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	603 if(rnaseq.gb) {
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	604 exonranges.list <- unlist(exonmodel[coord[i, ]$tid])
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	605 } else {
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	606 exonranges.list <- NULL
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	607 }
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	608 doCov(coord[i, ], exonranges.list, ...)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	609 }
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	610
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	611 # Floor negative values which are caused by spline.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	612 result.matrix[result.matrix < 0] <- 0
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	613 result.matrix / libsize * 1e6 # normalize to RPM.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	614
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	615 } else {
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	616 for(c in 1:length(chkidx.list)) {
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	617 chk <- chkidx.list[[c]]
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	618 i <- chk[1]:chk[2] # chunk: start -> end
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	619 cat(".")
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	620 # If RNA-seq, retrieve exon ranges.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	621 if(rnaseq.gb) {
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	622 exonranges.list <- unlist(exonmodel[coord[i, ]$tid])
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	623 } else {
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	624 exonranges.list <- NULL
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	625 }
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	626 cov <- doCov(coord[i, ], exonranges.list, ...)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	627 if(c == 1) {
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	628 result.matrix <- matrix(0, nrow=nrow(coord), ncol=ncol(cov))
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	629 }
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	630 result.matrix[i, ] <- cov
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	631 }
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	632 # Floor negative values which are caused by spline.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	633 # browser()
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	634 result.matrix[result.matrix < 0] <- 0
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	635 result.matrix / libsize * 1e6 # normalize to RPM.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	636
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	637 }
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	638 }
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	639
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	640
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	641 doCov <- function(coord.mat, exonranges.list, chr.tag, pint, reg2plot,
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	642 flanksize, flankfactor, m.pts, f.pts, ...) {
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	643 # Extract coverage from bam file into a matrix. According to the parameter
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	644 # values, call corresponding functions.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	645 # Args:
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	646 # coord.mat: matrix of genomic coordinates to extract coverage.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	647 # exonranges.list: list of IRanges objects, each represents a group of exons.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	648 # pint: boolean of point interval.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	649 # reg2plot: string of region to plot.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	650 # flanksize: flanking region size.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	651 # flankfactor: flanking region factor.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	652 # m.pts: data points for middle interval.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	653 # f.pts: data points for flanking region.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	654 # Return: matrix of interpolated coverage: each row represents a gene; each
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	655 # column represents a data point. Coverage from exons are concatenated.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	656
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	657 v.chrom <- coord.mat$chrom
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	658 # if(!chr.tag) {
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	659 # v.chrom <- sub('chr', '', v.chrom)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	660 # }
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	661 v.chrom <- as.factor(v.chrom)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	662 v.strand <- as.factor(coord.mat$strand)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	663
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	664 # Figure out interval region sizes and calculate flanking region sizes.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	665 if(!pint) { # interval regions.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	666 if(!is.null(exonranges.list)) { # RNA-seq
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	667 if(flankfactor > 0) {
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	668 v.fls <- sapply(exonranges.list, function(t) {
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	669 sum(end(t) - start(t) + 1) * flankfactor
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	670 })
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	671 } else {
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	672 v.fls <- rep(flanksize, length=nrow(coord.mat))
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	673 }
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	674 extrCovExons(v.chrom, exonranges.list, v.fls, v.strand,
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	675 m.pts, f.pts, ...)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	676 } else { # ChIP-seq with intervals.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	677 v.start <- coord.mat$start
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	678 v.end <- coord.mat$end
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	679 if(flankfactor > 0) {
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	680 v.fls <- round((v.end - v.start + 1) * flankfactor)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	681 } else {
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	682 v.fls <- rep(flanksize, length=nrow(coord.mat))
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	683 }
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	684 extrCov3Sec(v.chrom, v.start, v.end, v.fls, v.strand,
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	685 m.pts, f.pts, ...)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	686 }
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	687 } else { # point center with flanking regions.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	688 v.midp <- vector('integer', length=nrow(coord.mat))
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	689 for(r in 1:nrow(coord.mat)) {
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	690 if(reg2plot == 'tss' && v.strand[r] == '+' \|\|
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	691 reg2plot == 'tes' && v.strand[r] == '-') {
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	692 # the left site is center.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	693 v.midp[r] <- coord.mat$start[r]
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	694 } else { # this also includes BED supplied point center.
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	695 v.midp[r] <- coord.mat$end[r]
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	696 }
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	697 }
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	698 # browser()
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	699 extrCovMidp(v.chrom, v.midp, flanksize, v.strand, m.pts + f.pts*2, ...)
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	700 }
3ca58369469c planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/ngsplot commit b'e9fcc157a7f2f2fa9d6ac9a58d425ff17c975f5c\n' artbio parents: diff changeset	701 }

Mercurial > repos > artbio > ngsplot

annotate lib/coverage.r @ 0:3ca58369469c draft