Mercurial > repos > computational-metabolomics > mspurity_filterfragspectra

diff frag4feature.R @ 9:a8842e5e75a7 draft

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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit 20a48a1862267264f98b7c514287f9a5cba1143f
author computational-metabolomics
date Thu, 13 Jun 2024 11:43:16 +0000
parents a46824d13914
children
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--- a/frag4feature.R	Wed Jun 12 16:09:13 2024 +0000
+++ b/frag4feature.R	Thu Jun 13 11:43:16 2024 +0000
@@ -81,7 +81,11 @@
     if (class(xobject) == "XCMSnExp") {
         # Get the legacy xcmsSet object
         suppressWarnings(xset <- as(xobject, "xcmsSet"))
-        sampclass(xset) <- xset@phenoData$sample_group
+        if (!is.null(xset@phenoData$sample_group)) {
+            xcms::sampclass(xset) <- xset@phenoData$sample_group
+        } else {
+            xcms::sampclass(xset) <- "."
+        }
         return(xset)
     }
 }
@@ -96,6 +100,7 @@
 print(pa@fileList)
 print(xset@filepaths)
 
+
 if (is.null(opt$intense)) {
     intense <- FALSE
 } else {