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comparison ruvseq.R @ 4:3a083c78896e draft default tip

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ruvseq commit 30117fce22f3771c9c0c13e70c3ad14b694de6e2
author iuc
date Fri, 21 Apr 2023 14:09:17 +0000
parents fed9d0350d72
children
comparison
equal deleted inserted replaced
3:d1f7fa5bb3cb 4:3a083c78896e
1 # setup R error handling to go to stderr 1 # setup R error handling to go to stderr
2 library("getopt") 2 library("getopt")
3 options(show.error.messages = F, error = function() { 3 options(show.error.messages = FALSE, error = function() {
4 cat(geterrmessage(), file = stderr()); q("no", 1, F) 4 cat(geterrmessage(), file = stderr())
5 q("no", 1, FALSE)
5 }) 6 })
6 options(stringAsFactors = FALSE, useFancyQuotes = FALSE) 7 options(stringAsFactors = FALSE, useFancyQuotes = FALSE)
7 8
8 setup_cmdline_options <- function() { 9 setup_cmdline_options <- function() {
9 args <- commandArgs(trailingOnly = TRUE) 10 args <- commandArgs(trailingOnly = TRUE)
15 "max_k", "max_k", 1, "double", 16 "max_k", "max_k", 1, "double",
16 "sample_json", "s", 1, "character", 17 "sample_json", "s", 1, "character",
17 "plots", "p", 1, "character", 18 "plots", "p", 1, "character",
18 "header", "H", 0, "logical", 19 "header", "H", 0, "logical",
19 "txtype", "y", 1, "character", 20 "txtype", "y", 1, "character",
20 "tx2gene", "x", 1, "character"), # a space-sep tx-to-gene map or GTF file (auto detect .gtf/.GTF) 21 "tx2gene", "x", 1, "character", # a space-sep tx-to-gene map or GTF file (auto detect .gtf/.GTF)
22 "ruv_ncounts", "ruv_ncounts", 0, "logical"),
21 byrow = TRUE, ncol = 4) 23 byrow = TRUE, ncol = 4)
22 24
23 opt <- getopt(spec) 25 opt <- getopt(spec)
24 # if help was asked for print a friendly message 26 # if help was asked for print a friendly message
25 # and exit with a non-zero error code 27 # and exit with a non-zero error code
153 opt <- setup_cmdline_options() 155 opt <- setup_cmdline_options()
154 alpha <- opt$alpha 156 alpha <- opt$alpha
155 min_k <- opt$min_k 157 min_k <- opt$min_k
156 max_k <- opt$max_k 158 max_k <- opt$max_k
157 min_c <- opt$min_mean_count 159 min_c <- opt$min_mean_count
160 ruv_ncounts <- ifelse(is.null(opt$ruv_ncounts), FALSE, TRUE)
158 sample_json <- fromJSON(opt$sample_json) 161 sample_json <- fromJSON(opt$sample_json)
159 sample_paths <- sample_json$path 162 sample_paths <- sample_json$path
160 sample_names <- sample_json$label 163 sample_names <- sample_json$label
161 condition <- as.factor(sample_json$condition) 164 condition <- as.factor(sample_json$condition)
162 sample_table <- data.frame(samplename = sample_names, filename = sample_paths, condition = condition) 165 sample_table <- data.frame(samplename = sample_names, filename = sample_paths, condition = condition)
181 set <- result[[name]] 184 set <- result[[name]]
182 unwanted_variation <- pData(set) 185 unwanted_variation <- pData(set)
183 df <- data.frame(identifier = rownames(unwanted_variation)) 186 df <- data.frame(identifier = rownames(unwanted_variation))
184 df <- cbind(df, unwanted_variation) 187 df <- cbind(df, unwanted_variation)
185 colnames(df)[2] <- "condition" 188 colnames(df)[2] <- "condition"
186 write.table(df, file = paste0("batch_effects_", name, ".tabular"), sep = "\t", quote = F, row.names = F) 189 write.table(df, file = paste0("uv_batch_effects_", name, ".tabular"), sep = "\t", quote = FALSE, row.names = FALSE)
190 if (ruv_ncounts) {
191 ruvnorm_counts <- normCounts(set)
192 ruvnorm_df <- data.frame(geneID = rownames(ruvnorm_counts), ruvnorm_counts)
193 write.table(ruvnorm_df, file = paste0("ruv_norm_counts_", name, ".tabular"), sep = "\t", quote = FALSE, row.names = FALSE)
194 }
187 } 195 }
196
188 } 197 }
189 198
190 # close the plot device 199 # close the plot device
191 if (!is.null(opt$plots)) { 200 if (!is.null(opt$plots)) {
192 cat("closing plot device\n") 201 cat("closing plot device\n")