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comparison edger.R @ 12:a8305cf0c951 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 4955aeed800ea8e45057b7e8578dc878a07f9cfc
author iuc
date Thu, 21 Sep 2023 10:01:55 +0000
parents 6e53e565fc6a
children 0cb907a2a810
comparison
equal deleted inserted replaced
11:f2843df56434 12:a8305cf0c951
38 38
39 # Record starting time 39 # Record starting time
40 time_start <- as.character(Sys.time()) 40 time_start <- as.character(Sys.time())
41 41
42 # setup R error handling to go to stderr 42 # setup R error handling to go to stderr
43 options(show.error.messages = F, error = function() { 43 options(show.error.messages = FALSE, error = function() {
44 cat(geterrmessage(), file = stderr()) 44 cat(geterrmessage(), file = stderr())
45 q("no", 1, F) 45 q("no", 1, FALSE)
46 }) 46 })
47 47
48 # we need that to not crash galaxy with an UTF8 error on German LC settings. 48 # we need that to not crash galaxy with an UTF8 error on German LC settings.
49 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8") 49 loc <- Sys.setlocale("LC_MESSAGES", "en_US.UTF-8")
50 50
103 if (file == "") { 103 if (file == "") {
104 file <- stdout() 104 file <- stdout()
105 } else if (substring(file, 1L, 1L) == "|") { 105 } else if (substring(file, 1L, 1L) == "|") {
106 file <- pipe(substring(file, 2L), "w") 106 file <- pipe(substring(file, 2L), "w")
107 on.exit(close(file)) 107 on.exit(close(file))
108 } 108 } else {
109 else {
110 file <- file(file, ifelse(append, "a", "w")) 109 file <- file(file, ifelse(append, "a", "w"))
111 on.exit(close(file)) 110 on.exit(close(file))
112 } 111 }
113 } 112 }
114 .Internal(cat(list(...), file, sep, fill, labels, append)) 113 .Internal(cat(list(...), file, sep, fill, labels, append))
179 byrow = TRUE, ncol = 4 178 byrow = TRUE, ncol = 4
180 ) 179 )
181 opt <- getopt(spec) 180 opt <- getopt(spec)
182 181
183 182
184 if (is.null(opt$matrixPath) & is.null(opt$filesPath)) { 183 if (is.null(opt$matrixPath) && is.null(opt$filesPath)) {
185 cat("A counts matrix (or a set of counts files) is required.\n") 184 cat("A counts matrix (or a set of counts files) is required.\n")
186 q(status = 1) 185 q(status = 1)
187 } 186 }
188 187
189 if (is.null(opt$cpmReq)) { 188 if (is.null(opt$cpmReq)) {
385 postfilter_count <- nrow(data$counts) 384 postfilter_count <- nrow(data$counts)
386 filtered_count <- prefilter_count - postfilter_count 385 filtered_count <- prefilter_count - postfilter_count
387 386
388 # Name rows of factors according to their sample 387 # Name rows of factors according to their sample
389 row.names(factors) <- names(data$counts) 388 row.names(factors) <- names(data$counts)
390 factor_list <- sapply(names(factors), paste_listname) 389 factor_list <- names(factors)
391 390
392 # Generating the DGEList object "data" 391 # Generating the DGEList object "data"
393 samplenames <- colnames(data$counts) 392 samplenames <- colnames(data$counts)
394 genes <- data$genes 393 genes <- data$genes
395 data <- DGEList(data$counts) 394 data <- DGEList(data$counts)
403 for (i in seq_along(factor_list)) { 402 for (i in seq_along(factor_list)) {
404 formula <- paste(formula, factor_list[i], sep = "+") 403 formula <- paste(formula, factor_list[i], sep = "+")
405 } 404 }
406 405
407 formula <- formula(formula) 406 formula <- formula(formula)
408 design <- model.matrix(formula) 407 design <- model.matrix(formula, factors)
409 408
410 for (i in seq_along(factor_list)) { 409 for (i in seq_along(factor_list)) {
411 colnames(design) <- gsub(factor_list[i], "", colnames(design), fixed = TRUE) 410 colnames(design) <- gsub(factor_list[i], "", colnames(design), fixed = TRUE)
412 } 411 }
413 412