diff edger.R @ 15:119f41ec0ada draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/edger commit 76bd257ee51e9d7b912f570fb9ced1084ef44212

--- a/edger.R	Wed Sep 04 15:49:53 2024 +0000
+++ b/edger.R	Wed Oct 15 10:24:03 2025 +0000
@@ -330,6 +330,8 @@
 }
 contrast_data <- sanitise_equation(contrast_data)
 contrast_data <- gsub(" ", ".", contrast_data, fixed = TRUE)
+# Convert colons to dots to match design matrix column name processing
+contrast_data <- gsub(":", ".", contrast_data, fixed = TRUE)
 
 bcv_pdf <- make_out("bcvplot.pdf")
 bcv_png <- make_out("bcvplot.png")
@@ -431,6 +433,9 @@
     colnames(design) <- gsub(factor_list[i], "", colnames(design), fixed = TRUE)
 }
 
+# Ensure column names are syntactically valid
+colnames(design) <- make.names(colnames(design))
+
 # Calculating normalising factor, estimating dispersion
 data <- calcNormFactors(data, method = opt$normOpt)