Mercurial > repos > tomnl > mspurity_createmsp

diff createDatabase.R @ 11:4b3b0f5a55d9 draft

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planemo upload for repository https://github.com/computational-metabolomics/mspurity-galaxy commit b6b8da66a6eef180ca8e333f98fc4b7575bac7b3
author tomnl
date Thu, 27 Jun 2019 12:34:09 -0400
parents e6a78f89ee07
children
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--- a/createDatabase.R	Tue Jun 25 12:34:19 2019 -0400
+++ b/createDatabase.R	Thu Jun 27 12:34:09 2019 -0400
@@ -154,15 +154,13 @@
   }
 
   xset@peaks <- as.matrix(plyr::ddply(data.frame(xset@peaks), ~ sample, convert2Raw, xset=xset))
-  
+
   # Saves the EICS into the previously created database
-  xgroups <-  as.numeric(as.character(unique(pa@grped_df$grpid)))
-  px <- msPurity::purityX(xset, 
+  px <- msPurity::purityX(xset,
                           saveEIC = TRUE,
                           cores=1,
                           sqlitePth=dbPth,
-                          rtrawColumns = TRUE, 
-                          xgroups = xgroups)
+                          rtrawColumns = TRUE)
 
 }