Mercurial > repos > lecorguille > xcms_retcor

diff xcms_retcor.r @ 23:faf4a6b67304 draft

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"planemo upload for repository https://github.com/workflow4metabolomics/xcms commit 665b0684ed3cd1db5d297e0265c59787f8b66289"
author workflow4metabolomics
date Thu, 13 Feb 2020 06:43:08 -0500
parents 972e76582173
children aa252eec9229
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line diff
--- a/xcms_retcor.r	Wed Feb 12 08:30:30 2020 -0500
+++ b/xcms_retcor.r	Thu Feb 13 06:43:08 2020 -0500
@@ -63,6 +63,12 @@
 
 adjustRtimeParam <- do.call(paste0(method,"Param"), args)
 print(adjustRtimeParam)
+
+if (hasAdjustedRtime(xdata)) {
+  cat("WARNING: a retention time ajustment had already been applied to your data.\nThe function applyAdjustedRtime was processed to cumulate the ajustment")
+  cat("Replace raw retention times with adjusted retention times.\n")
+  xdata <- applyAdjustedRtime(xdata)
+}
 xdata <- adjustRtime(xdata, param=adjustRtimeParam)
 
 #cat("\t\t\tCompute and Store TIC and BPI\n")