add header line to deg counts file

R-ODAF · Oct 3, 2024 · 18bea3c · 18bea3c
1 parent 041f370
commit 18bea3c
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Showing 2 changed files with 3 additions and 2 deletions.
diff --git a/Rmd/summary_report_new.Rmd b/Rmd/summary_report_new.Rmd
@@ -323,7 +323,7 @@ A count matrix containing the $`r num_passed_total`$ samples that passed QC was
 # read in contrasts
 exp_contrasts <- R.ODAF.utils::get_contrasts(file.path(paths$contrasts, params$contrasts_file), paths)
 
-deg_counts <- read.delim(file.path(paths$summary, "DEG_counts.txt"), sep = "\t", stringsAsFactors = FALSE, header = FALSE)
+deg_counts <- read.delim(file.path(paths$summary, "DEG_counts.txt"), sep = "\t", stringsAsFactors = FALSE, header = TRUE)
 
 if (!is.na(params$reports_facet)) {
   colnames(deg_counts) <- c(params$reports_facet, "Contrast", "DEGs", "Downregulated", "Upregulated")

diff --git a/scripts/run_DESeq2.R b/scripts/run_DESeq2.R
@@ -184,6 +184,7 @@ if (params$parallel) {
   )
 }
 
+# Write summary counts to a file
 write.table(summary_counts,
             file = file.path(paths$summary, "DEG_counts.txt"),
-            quote = FALSE, sep = "\t", col.names = FALSE, row.names = FALSE)
+            quote = FALSE, sep = "\t", col.names = TRUE, row.names = FALSE)