rna_probing: normalize.R annotate

annotate normalize.R @ 24:431aebd93843 draft default tip

Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files.

author	nikos
date	Wed, 05 Aug 2015 09:21:02 -0400
parents
children

rev	line source
24 431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	1 ##!/usr/bin/Rscript
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	2
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	3 ## Setup R error handling to go to stderr
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	4 options( show.error.messages = FALSE, error = function () { cat( geterrmessage(), file=stderr() ); q( "no", 1, F ) } )
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	5
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	6 # we need that to not crash galaxy with an UTF8 error on LC settings.
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	7 Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	8
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	9 suppressMessages(library('getopt'))
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	10
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	11 #get options, using the spec as defined by the enclosed list.
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	12 #we read the options from the default: commandArgs(TRUE).
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	13 spec = matrix(c(
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	14 'treated', 't', 1, "character",
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	15 'control', 'c', 2, "character",
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	16 'method', 'm', 1, "character",
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	17 'fuComplexity', 'b', 2, "integer",
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	18 'k2nTreated', 'k', 2, "character",
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	19 'k2nControl', 'a', 2, "character",
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	20 'cutoff', 'g', 1, "integer",
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	21 'reference', 'r', 2, "character",
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	22 'compdata', 'h', 2, "character",
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	23 'dtcr', 'd', 0, "logical",
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	24 'dtcrWindow', 'e', 2, "integer",
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	25 'dtcrToZero', 'f', 2, "character",
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	26 'slograt', 's', 0, "logical",
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	27 'slogratWindow', 'p', 2, "integer",
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	28 'depthCorrection', 'q', 2, "character",
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	29 'pseudocount', 'l', 2, "integer",
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	30 'swinsor', 'w', 0, "logical",
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	31 'swinsorWindow', 'x', 2, "integer",
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	32 'winsorLevel', 'y', 2, "double",
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	33 'fixQuantile', 'z', 2, "character",
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	34 'ntOffset', 'n', 2, "integer",
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	35 'outputDir', 'o', 1, "character",
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	36 'bedgraph', 'v', 2, "character",
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	37 'bed', 'j', 2, "character",
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	38 'genome', 'i', 2, "character",
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	39 'trackName', 'u', 2, "character"
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	40 ), byrow=TRUE, ncol=4);
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	41
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	42 opt = getopt(spec);
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	43
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	44 suppressMessages(require(RNAprobR))
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	45
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	46
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	47 #Create output dir
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	48 dir.create(opt$outputDir, showWarnings = FALSE, recursive = TRUE)
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	49
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	50
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	51 if (opt$method=="counts"){
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	52 treated_euc <- readsamples(opt$treated, euc=opt$method)
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	53 } else if (opt$method=="Fu") {
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	54 treated_euc <- readsamples(opt$treated, euc=opt$method, m = opt$fuComplexity)
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	55 } else {
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	56 treated_euc <- readsamples(opt$treated, euc=opt$method, k2n_files=opt$k2nTreated)
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	57 }
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	58
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	59
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	60 if ( !is.null(opt$reference)){
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	61 comp_treated <- comp(treated_euc, cutoff=opt$cutoff,
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	62 fasta_file=opt$reference)
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	63 } else {
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	64 comp_treated <- comp(treated_euc, cutoff=opt$cutoff)
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	65 }
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	66
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	67
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	68 #If present, read control file
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	69 if ( !is.null(opt$control) && opt$control != 'None'){
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	70 if (opt$method=="counts"){
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	71 control_euc <- readsamples(opt$control, euc=opt$method)
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	72 } else if (opt$method=="Fu") {
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	73 control_euc <- readsamples(opt$control, euc=opt$method, m = opt$fuComplexity)
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	74 } else {
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	75 control_euc <- readsamples(opt$control, euc=opt$method, k2n_files=opt$k2nControl)
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	76 }
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	77 if ( !is.null(opt$reference)){
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	78 comp_control <- comp(control_euc, cutoff=opt$cutoff,
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	79 fasta_file=opt$reference)
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	80 } else {
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	81 comp_control <- comp(control_euc, cutoff=opt$cutoff)
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	82 }
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	83 }
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	84
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	85 #compdata
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	86 if ( !is.null(opt$compdata) ) {
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	87
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	88 normalized <- compdata(comp_treated, nt_offset=opt$ntOffset)
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	89 colnames(mcols(normalized))[1:4] <- paste(colnames(mcols(normalized))[1:4], ".treated", sep="")
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	90
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	91 if ( !is.null(opt$control) && opt$control != 'None') {
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	92 normalized <- compdata(comp_control, nt_offset=opt$ntOffset, add_to=normalized)
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	93 colnames(mcols(normalized))[6:9] <- c("TC.control", "TCR.control", "Cover.control", "PC.control")
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	94 }
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	95 }
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	96
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	97 #dtcr
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	98 if ( !is.null(opt$dtcr) ) {
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	99 if ( exists("normalized")) {
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	100 normalized <- dtcr(comp_control, comp_treated, window_size=opt$dtcrWindow,
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	101 nt_offset=opt$ntOffset, bring_to_zero=opt$dtcrToZero,
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	102 add_to=normalized)
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	103 }
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	104 else {
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	105 normalized <- dtcr(comp_control, comp_treated, window_size=opt$dtcrWindow,
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	106 nt_offset=opt$ntOffset, bring_to_zero=opt$dtcrToZero)
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	107 }
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	108 }
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	109
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	110 #slograt
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	111 if ( !is.null(opt$slograt) ) {
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	112 if ( exists("normalized")) {
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	113 normalized <- slograt(comp_control, comp_treated, window_size=opt$slogratWindow,
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	114 nt_offset=opt$ntOffset, depth_correction = opt$depthCorrection,
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	115 pseudocount=opt$pseudocount, add_to=normalized)
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	116 }
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	117 else {
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	118 normalized <- slograt(comp_control, comp_treated, window_size=opt$slogratWindow,
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	119 nt_offset=opt$ntOffset, depth_correction = opt$depthCorrection,
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	120 pseudocount=opt$pseudocount)
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	121 }
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	122 }
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	123
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	124 #swinsor
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	125 if ( !is.null(opt$swinsor) ) {
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	126 if ( exists("normalized")) {
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	127 normalized <- swinsor(comp_treated, winsor_level = opt$winsorLevel,
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	128 window_size=opt$swinsorWindow,
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	129 only_top=opt$fixQuantile, nt_offset=opt$ntOffset,
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	130 add_to=normalized)
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	131 }
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	132 else {
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	133 normalized <- swinsor(comp_treated, winsor_level = opt$winsorLevel,
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	134 window_size=opt$swinsorWindow,
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	135 only_top=opt$fixQuantile, nt_offset=opt$ntOffset)
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	136 }
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	137 }
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	138
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	139 #bedgraph output
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	140 if ( !is.null(opt$bedgraph)) {
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	141 if ( !is.null(opt$dtcr)){
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	142 norm2bedgraph(normalized, bed_file = opt$bed, norm_method = "dtcr",
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	143 genome_build = opt$genome,
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	144 bedgraph_out_file = paste(opt$outputDir, "/dtcr",
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	145 sep=""),
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	146 track_name = opt$trackName,
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	147 track_description = opt$trackDesc)
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	148 }
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	149 if ( !is.null(opt$slograt)){
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	150 norm2bedgraph(normalized, bed_file = opt$bed, norm_method = "slograt",
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	151 genome_build = opt$genome,
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	152 bedgraph_out_file = paste(opt$outputDir, "/slograt",
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	153 sep=""),
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	154 track_name = opt$trackName,
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	155 track_description = opt$trackDesc)
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	156 }
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	157 if ( !is.null(opt$swinsor)){
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	158 norm2bedgraph(normalized, bed_file = opt$bed, norm_method = "swinsor",
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	159 genome_build = opt$genome,
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	160 bedgraph_out_file = paste(opt$outputDir, "/swinsor",
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	161 sep=""),
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	162 track_name = opt$trackName,
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	163 track_description = opt$trackDesc)
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	164 }
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	165 }
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	166
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	167 output <- GR2norm_df(normalized)
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	168 write.table( output, paste(opt$outputDir, "/norm_df.txt", sep = ""), sep = "\t",
431aebd93843 Fixed a bug in k2n.R where the function k2n_calc() would result in an error for single-end read files. nikos parents: diff changeset	169 quote = F, row.names = F)

Mercurial > repos > nikos > rna_probing

annotate normalize.R @ 24:431aebd93843 draft default tip