Mercurial > repos > iuc > limma_voom

comparison limma_voom.R @ 19:c9c6427edfe9 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 4c0406815cb76175d7d90b2874310635694126f5
author iuc
date Tue, 28 May 2019 10:04:10 -0400
parents 97e06a4c7c75
children 0921444c832d
comparison
equal deleted inserted replaced
18:97e06a4c7c75 19:c9c6427edfe9
7 # filesPath", "j", 2, "character" -JSON list object if multiple files input 7 # filesPath", "j", 2, "character" -JSON list object if multiple files input
8 # matrixPath", "m", 2, "character" -Path to count matrix 8 # matrixPath", "m", 2, "character" -Path to count matrix
9 # factFile", "f", 2, "character" -Path to factor information file 9 # factFile", "f", 2, "character" -Path to factor information file
10 # factInput", "i", 2, "character" -String containing factors if manually input 10 # factInput", "i", 2, "character" -String containing factors if manually input
11 # annoPath", "a", 2, "character" -Path to input containing gene annotations 11 # annoPath", "a", 2, "character" -Path to input containing gene annotations
12 # contrastData", "C", 1, "character" -String containing contrasts of interest 12 # contrastFile", "C", 1, "character" -Path to contrasts information file
13 # contrastInput", "D", 1, "character" -String containing contrasts of interest
13 # cpmReq", "c", 2, "double" -Float specifying cpm requirement 14 # cpmReq", "c", 2, "double" -Float specifying cpm requirement
14 # cntReq", "z", 2, "integer" -Integer specifying minimum total count requirement 15 # cntReq", "z", 2, "integer" -Integer specifying minimum total count requirement
15 # sampleReq", "s", 2, "integer" -Integer specifying cpm requirement 16 # sampleReq", "s", 2, "integer" -Integer specifying cpm requirement
16 # normCounts", "x", 0, "logical" -String specifying if normalised counts should be output 17 # normCounts", "x", 0, "logical" -String specifying if normalised counts should be output
17 # rdaOpt", "r", 0, "logical" -String specifying if RData should be output 18 # rdaOpt", "r", 0, "logical" -String specifying if RData should be output
159 "filesPath", "j", 2, "character", 160 "filesPath", "j", 2, "character",
160 "matrixPath", "m", 2, "character", 161 "matrixPath", "m", 2, "character",
161 "factFile", "f", 2, "character", 162 "factFile", "f", 2, "character",
162 "factInput", "i", 2, "character", 163 "factInput", "i", 2, "character",
163 "annoPath", "a", 2, "character", 164 "annoPath", "a", 2, "character",
164 "contrastData", "C", 1, "character", 165 "contrastFile", "C", 1, "character",
166 "contrastInput", "D", 1, "character",
165 "cpmReq", "c", 1, "double", 167 "cpmReq", "c", 1, "double",
166 "totReq", "y", 0, "logical", 168 "totReq", "y", 0, "logical",
167 "cntReq", "z", 1, "integer", 169 "cntReq", "z", 1, "integer",
168 "sampleReq", "s", 1, "integer", 170 "sampleReq", "s", 1, "integer",
169 "filtCounts", "F", 0, "logical", 171 "filtCounts", "F", 0, "logical",
341 } 343 }
342 344
343 #Create output directory 345 #Create output directory
344 dir.create(opt$outPath, showWarnings=FALSE) 346 dir.create(opt$outPath, showWarnings=FALSE)
345 347
346 # Split up contrasts seperated by comma into a vector then sanitise 348 # Process contrasts
347 contrastData <- unlist(strsplit(opt$contrastData, split=",")) 349 if (is.null(opt$contrastInput)) {
350 contrastData <- read.table(opt$contrastFile, header=TRUE, sep="\t", quote= "", strip.white=TRUE, stringsAsFactors=FALSE)
351 contrastData <- contrastData[, 1, drop=TRUE]
352 } else {
353 # Split up contrasts seperated by comma into a vector then sanitise
354 contrastData <- unlist(strsplit(opt$contrastInput, split=","))
355 }
356
357 # in case input groups start with numbers this will make the names valid R names, required for makeContrasts
348 contrastData <- sanitiseEquation(contrastData) 358 contrastData <- sanitiseEquation(contrastData)
349 contrastData <- gsub(" ", ".", contrastData, fixed=TRUE) 359 contrastData <- gsub(" ", ".", contrastData, fixed=TRUE)
350 # in case input groups start with numbers this will make the names valid R names, required for makeContrasts
351 cons <- NULL 360 cons <- NULL
352 for (i in contrastData) { 361 for (i in contrastData) {
353 i <- strsplit(i, split="-") 362 i <- strsplit(i, split="-")
354 i <- lapply(i, make.names) 363 i <- lapply(i, make.names)
355 i <- lapply(i, paste, collapse="-") 364 i <- lapply(i, paste, collapse="-")