frag4feature: anticipated_purity

annotate anticipated_purity_lcms.R @ 3:8a9f643e8023 draft

planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty

author	tomnl
date	Tue, 27 Mar 2018 11:46:31 -0400
parents	15aa034cc08d
children	e94ce372d03d

rev	line source
0 15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	1 library(msPurity)
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	2 library(optparse)
3 8a9f643e8023 planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 2e847122cf605951c334858455fc1d3ebdb189e9-dirty tomnl parents: 0 diff changeset	3 print(sessionInfo())
0 15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	4
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	5 option_list <- list(
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	6 make_option(c("--xset_path"), type="character"),
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	7 make_option(c("-o", "--out_dir"), type="character"),
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	8 make_option(c("--mzML_path"), type="character"),
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	9 make_option("--minOffset", default=0.5),
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	10 make_option("--maxOffset", default=0.5),
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	11 make_option("--ilim", default=0.05),
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	12 make_option("--iwNorm", default="none", type="character"),
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	13 make_option("--exclude_isotopes", action="store_true"),
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	14 make_option("--isotope_matrix", type="character"),
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	15 make_option("--purityType", default="purityFWHMmedian"),
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	16 make_option("--singleFile", default=0),
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	17 make_option("--cores", default=4),
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	18 make_option("--xgroups", type="character"),
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	19 make_option("--rdata_name", default='xset'),
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	20 make_option("--camera_xcms", default='xset'),
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	21 make_option("--files", type="character"),
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	22 make_option("--galaxy_files", type="character"),
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	23 make_option("--choose_class", type="character"),
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	24 make_option("--ignore_files", type="character"),
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	25 make_option("--rtraw_columns", action="store_true")
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	26 )
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	27
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	28 # store options
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	29 opt<- parse_args(OptionParser(option_list=option_list))
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	30
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	31 print(sessionInfo())
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	32 print(opt)
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	33
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	34 if (!is.null(opt$xgroups)){
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	35 xgroups = as.numeric(strsplit(opt$xgroups, ',')[[1]])
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	36 }else{
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	37 xgroups = NULL
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	38 }
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	39
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	40
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	41
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	42 print(xgroups)
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	43
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	44 if (!is.null(opt$remove_nas)){
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	45 df <- df[!is.na(df$mz),]
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	46 }
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	47
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	48 if (is.null(opt$isotope_matrix)){
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	49 im <- NULL
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	50 }else{
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	51 im <- read.table(opt$isotope_matrix,
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	52 header = TRUE, sep='\t', stringsAsFactors = FALSE)
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	53 }
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	54
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	55 if (is.null(opt$exclude_isotopes)){
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	56 isotopes <- FALSE
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	57 }else{
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	58 isotopes <- TRUE
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	59 }
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	60
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	61 if (is.null(opt$rtraw_columns)){
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	62 rtraw_columns <- FALSE
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	63 }else{
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	64 rtraw_columns <- TRUE
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	65 }
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	66
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	67 loadRData <- function(rdata_path, xset_name){
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	68 #loads an RData file, and returns the named xset object if it is there
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	69 load(rdata_path)
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	70 print(ls())
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	71 return(get(ls()[ls() == xset_name]))
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	72 }
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	73
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	74 target_obj <- loadRData(opt$xset_path, opt$rdata_name)
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	75
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	76 if (opt$camera_xcms=='camera'){
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	77 xset <- target_obj@xcmsSet
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	78 }else{
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	79 xset <- target_obj
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	80 }
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	81
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	82 print(xset)
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	83
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	84 minOffset = as.numeric(opt$minOffset)
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	85 maxOffset = as.numeric(opt$maxOffset)
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	86
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	87
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	88 if (opt$iwNorm=='none'){
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	89 iwNorm = FALSE
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	90 iwNormFun = NULL
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	91 }else if (opt$iwNorm=='gauss'){
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	92 iwNorm = TRUE
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	93 iwNormFun = msPurity::iwNormGauss(minOff=-minOffset, maxOff=maxOffset)
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	94 }else if (opt$iwNorm=='rcosine'){
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	95 iwNorm = TRUE
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	96 iwNormFun = msPurity::iwNormRcosine(minOff=-minOffset, maxOff=maxOffset)
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	97 }else if (opt$iwNorm=='QE5'){
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	98 iwNorm = TRUE
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	99 iwNormFun = msPurity::iwNormQE.5()
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	100 }
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	101
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	102 print(xset@filepaths)
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	103
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	104
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	105
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	106 if (!is.null(opt$files)){
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	107 updated_filepaths <- trimws(strsplit(opt$files, ',')[[1]])
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	108 updated_filepaths <- updated_filepaths[updated_filepaths != ""]
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	109 print(updated_filepaths)
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	110 updated_filenames = basename(updated_filepaths)
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	111 original_filenames = basename(xset@filepaths)
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	112 update_idx = match(updated_filenames, original_filenames)
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	113
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	114 if (!is.null(opt$galaxy_files)){
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	115 galaxy_files <- trimws(strsplit(opt$galaxy_files, ',')[[1]])
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	116 galaxy_files <- galaxy_files[galaxy_files != ""]
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	117 xset@filepaths <- galaxy_files[update_idx]
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	118 }else{
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	119 xset@filepaths <- updated_filepaths[update_idx]
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	120 }
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	121 }
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	122
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	123 if (!is.null(opt$choose_class)){
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	124 classes <- trimws(strsplit(opt$choose_class, ',')[[1]])
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	125
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	126
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	127 ignore_files_class <- which(!as.character(xset@phenoData$class) %in% classes)
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	128
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	129 print('choose class')
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	130 print(ignore_files_class)
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	131 }else{
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	132 ignore_files_class <- NA
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	133 }
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	134
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	135 if (!is.null(opt$ignore_files)){
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	136 ignore_files_string <- trimws(strsplit(opt$ignore_files, ',')[[1]])
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	137 filenames <- rownames(xset@phenoData)
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	138 ignore_files <- which(filenames %in% ignore_files_string)
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	139
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	140 ignore_files <- unique(c(ignore_files, ignore_files_class))
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	141 ignore_files <- ignore_files[ignore_files != ""]
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	142 }else{
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	143 if (anyNA(ignore_files_class)){
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	144 ignore_files <- NULL
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	145 }else{
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	146 ignore_files <- ignore_files_class
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	147 }
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	148
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	149 }
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	150
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	151 print('ignore_files')
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	152 print(ignore_files)
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	153
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	154
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	155 ppLCMS <- msPurity::purityX(xset=xset,
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	156 offsets=c(minOffset, maxOffset),
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	157 cores=opt$cores,
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	158 xgroups=xgroups,
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	159 purityType=opt$purityType,
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	160 ilim = opt$ilim,
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	161 isotopes = isotopes,
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	162 im = im,
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	163 iwNorm = iwNorm,
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	164 iwNormFun = iwNormFun,
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	165 singleFile = opt$singleFile,
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	166 fileignore = ignore_files,
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	167 rtraw_columns=rtraw_columns)
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	168
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	169
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	170 dfp <- ppLCMS@predictions
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	171
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	172 # to make compatable with deconrank
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	173 colnames(dfp)[colnames(dfp)=='grpid'] = 'peakID'
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	174 colnames(dfp)[colnames(dfp)=='median'] = 'medianPurity'
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	175 colnames(dfp)[colnames(dfp)=='mean'] = 'meanPurity'
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	176 colnames(dfp)[colnames(dfp)=='sd'] = 'sdPurity'
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	177 colnames(dfp)[colnames(dfp)=='stde'] = 'sdePurity'
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	178 colnames(dfp)[colnames(dfp)=='RSD'] = 'cvPurity'
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	179 colnames(dfp)[colnames(dfp)=='pknm'] = 'pknmPurity'
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	180 if(sum(is.na(dfp$medianPurity))>0){
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	181 dfp[is.na(dfp$medianPurity),]$medianPurity = 0
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	182 }
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	183
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	184 print('saving tsv')
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	185 print(head(dfp))
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	186 write.table(dfp, file.path(opt$out_dir, 'anticipated_purity_lcms.tsv'), row.names=FALSE, sep='\t')
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	187 print('saving RData')
15aa034cc08d planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit f9591483bef88aef71a9f0cc0ffc75cf6eab480c tomnl parents: diff changeset	188 save.image(file.path(opt$out_dir, 'anticipated_purity_lcms.RData'))

Mercurial > repos > tomnl > frag4feature

annotate anticipated_purity_lcms.R @ 3:8a9f643e8023 draft