Mercurial > repos > eschen42 > mqppep_preproc

diff MaxQuantProcessingScript.R @ 6:42daf70d4ed4 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tree/master/tools/mqppep commit 9dfb7e07a3673d7de4b0a1b7e6ce1b75a8a4f42b"
author eschen42
date Fri, 11 Mar 2022 20:04:40 +0000
parents b91809a18dbe
children 36f183e5e4ed
line wrap: on
line diff
--- a/MaxQuantProcessingScript.R	Thu Mar 10 23:43:38 2022 +0000
+++ b/MaxQuantProcessingScript.R	Fri Mar 11 20:04:40 2022 +0000
@@ -521,6 +521,14 @@
 # ---
 quant_write <- cbind(metadata_df[, "Sequence window"], quant_data)
 colnames(quant_write)[1] <- "Sequence.Window"
+write.table(
+  quant_write,
+  file = quant_file_name,
+  sep = "\t",
+  quote = FALSE,
+  col.names = TRUE,
+  row.names = FALSE
+)
 # ...
 
 
@@ -568,14 +576,6 @@
 pct_multiphos <- sprintf("%0.1f%s", 100 * pct_multiphos, "%")
 # ...
 
-write.table(
-  quant_data_qc_collapsed,
-  file = quant_file_name,
-  sep = "\t",
-  quote = FALSE,
-  col.names = TRUE,
-  row.names = FALSE
-)
 
 # Compute and visualize breakdown of pY, pS, and pT before enrichment filter
 # ---