Mercurial > repos > iuc > limma_voom

comparison limma_voom.R @ 2:a330ddf43861 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/limma_voom commit 346319bd01bfd51f02d656e653a93f0bd1e954aa
author iuc
date Thu, 07 Sep 2017 05:27:27 -0400
parents 76d01fe0ec36
children 38aab66ae5cb
comparison
equal deleted inserted replaced
1:76d01fe0ec36 2:a330ddf43861
154 normCounts <- as.character(argv[14]) 154 normCounts <- as.character(argv[14])
155 factPath <- as.character(argv[15]) 155 factPath <- as.character(argv[15])
156 # Process factors 156 # Process factors
157 if (as.character(argv[16])=="None") { 157 if (as.character(argv[16])=="None") {
158 factorData <- read.table(factPath, header=TRUE, sep="\t") 158 factorData <- read.table(factPath, header=TRUE, sep="\t")
159 factors <- factorData[,-1] 159 factors <- factorData[,-1, drop=FALSE]
160 } else { 160 } else {
161 factorData <- list() 161 factorData <- list()
162 for (i in 16:length(argv)) { 162 for (i in 16:length(argv)) {
163 newFact <- unlist(strsplit(as.character(argv[i]), split="::")) 163 newFact <- unlist(strsplit(as.character(argv[i]), split="::"))
164 factorData <- rbind(factorData, newFact) 164 factorData <- rbind(factorData, newFact)
568 cata("<table border=\"1\" cellpadding=\"3\">\n") 568 cata("<table border=\"1\" cellpadding=\"3\">\n")
569 cata("<tr>\n") 569 cata("<tr>\n")
570 TableHeadItem("SampleID") 570 TableHeadItem("SampleID")
571 TableHeadItem(names(factors)[1]," (Primary Factor)") 571 TableHeadItem(names(factors)[1]," (Primary Factor)")
572 572
573 for (i in names(factors)[2:length(names(factors))]) { 573 if (ncol(factors) > 1) {
574 TableHeadItem(i) 574
575 } 575 for (i in names(factors)[2:length(names(factors))]) {
576 cata("</tr>\n") 576 TableHeadItem(i)
577 }
578 cata("</tr>\n")
579 }
577 580
578 for (i in 1:nrow(factors)) { 581 for (i in 1:nrow(factors)) {
579 cata("<tr>\n") 582 cata("<tr>\n")
580 TableHeadItem(row.names(factors)[i]) 583 TableHeadItem(row.names(factors)[i])
581 for (j in 1:ncol(factors)) { 584 for (j in 1:ncol(factors)) {