Previous changeset 17:1b03f6232900 (2016-02-26) Next changeset 19:9442d1bf6d93 (2016-02-26) |
Commit message:
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/goseq_1_22_0 commit fdd0811efc61c31f88ff17096fbe8ee8cfacd766-dirty |
modified:
goseq.r goseq.xml |
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diff -r 1b03f6232900 -r 5fb82111ec62 goseq.r --- a/goseq.r Fri Feb 26 08:49:59 2016 -0500 +++ b/goseq.r Fri Feb 26 11:42:43 2016 -0500 |
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@@ -1,6 +1,6 @@ sink(stdout(), type = "message") -library(goseq) -library(optparse) +suppressWarnings(suppressMessages(library(goseq))) +suppressWarnings(suppressMessages(library(optparse))) option_list <- list( make_option(c("-d", "--dge_file"), type="character", help="Path to file with differential gene expression result"), @@ -34,15 +34,13 @@ sample_vs_wallenius_plot = args$sample_vs_wallenius_plot repcnt = args$repcnt - # format DE genes into vector suitable for use with goseq dge_table = read.delim(dge_file, header = TRUE, sep="\t", check.names = FALSE) genes = as.integer(dge_table[,p_adj_column]<p_adj_cutoff) names(genes) = dge_table[,1] # Assuming first row contains gene names # Get gene lengths - -if (length_file) { +if (length_file !=FALSE) { length_table = read.delim(length_file, header=TRUE, sep="\t", check.names=FALSE, row.names=TRUE) gene_lengths = length_table[names(genes),]$length } else { @@ -53,7 +51,7 @@ pdf(length_bias_plot) pwf=nullp(genes, genome, gene_id, gene_lengths) -dev.off() +message = dev.off() # wallenius approximation of p-values GO.wall=goseq(pwf, genome, gene_id) @@ -68,7 +66,7 @@ xlab="log10(Wallenius p-values)",ylab="log10(Sampling p-values)", xlim=c(-3,0)) abline(0,1,col=3,lty=2) - dev.off() + message = dev.off() write.table(GO.samp, sampling_tab, sep="\t", row.names = FALSE, quote = FALSE) } |
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diff -r 1b03f6232900 -r 5fb82111ec62 goseq.xml --- a/goseq.xml Fri Feb 26 08:49:59 2016 -0500 +++ b/goseq.xml Fri Feb 26 11:42:43 2016 -0500 |
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@@ -48,11 +48,11 @@ <data format="pdf" label="Plot P-value from sampling against wallenius distribution" name="sample_vs_wallenius_plot"> <filter>repcnt != 0</filter> </data> - <data format="tabular" label="Ranked category list - wallenius" name="wallenius_tab" /> + <data format="tabular" label="Ranked category list - no length bias correction" name="nobias_tab" /> <data format="tabular" label="Ranked category list - sampling" name="sampling_tab"> <filter>repcnt != 0</filter> </data> - <data format="tabular" label="Ranked category list - no length bias correction" name="nobias_tab" /> + <data format="tabular" label="Ranked category list - wallenius approx. of p-values" name="wallenius_tab" /> </outputs> <tests> <test> |