From b758b7369b1a4409f8b3cdd398908a5823bcbad3 Mon Sep 17 00:00:00 2001
From: ermueller <erik@east.de>
Date: Mon, 24 Mar 2014 00:57:18 +0100
Subject: [PATCH] Fixed the peaklist-workflow in msmsWorkflow
---
R/leMsMs.r | 16 ++++++++--------
R/leMsmsRaw.R | 3 +++
2 files changed, 11 insertions(+), 8 deletions(-)
diff --git a/R/leMsMs.r b/R/leMsMs.r
index 80aa23b..bf47762 100755
--- a/R/leMsMs.r
+++ b/R/leMsMs.r
@@ -158,17 +158,17 @@ msmsWorkflow <- function(w, mode="pH", steps=c(1:8), confirmMode = FALSE, newRec
for(i in 1:length(unique(cpdIDs))) {
indices <- sapply(splitfn,function(a){return(unique(cpdIDs)[i] %in% a)})
files[[i]] <- w@files[indices]
- }
+ }
- peaklist <- list()
+ peaklist <- list()
- for(i in 1:length(w@files)){
- peaklist[[1]] <- read.csv(w@files[i], header = TRUE)
- w <- addPeaksManually(w, cpdIDs[i], peaklist, mode=mode)
- }
- w@files <- sapply(files,function(files){return(files[1])})
- names(w@specs) <- basename(as.character(w@files))
+ for(i in 1:length(w@files)){
+ peaklist <- read.csv(w@files[i], header = TRUE)
+ w <- addPeaksManually(w, cpdIDs[i], peaklist, mode=mode)
}
+ w@files <- sapply(files,function(file){return(file[1])})
+ names(w@specs) <- basename(as.character(w@files))
+ }
}
# Step 2: first run analysis before recalibration
if(2 %in% steps)
diff --git a/R/leMsmsRaw.R b/R/leMsmsRaw.R
index 2ea94bf..2324867 100755
--- a/R/leMsmsRaw.R
+++ b/R/leMsmsRaw.R
@@ -623,9 +623,12 @@ addPeaksManually <- function(w, cpdID, handSpec, mode = "pH"){
} else {
pos <- which(pos)
w@specs[[pos]]$childHeaders <- rbind(w@specs[[pos]]$childHeaders,childHeader)
+ w@specs[[pos]]$childHeaders[,1] <- 2:(nrow(w@specs[[pos]]$childHeaders)+1)
+ w@specs[[pos]]$childHeaders[,2] <- w@specs[[pos]]$childHeaders[,1]
w@specs[[pos]]$childScans <- c(w@specs[[pos]]$childScans,max(w@specs[[pos]]$childScans)+1)
w@specs[[pos]]$peaks[[length(w@specs[[pos]]$peaks)+1]] <- handSpec
}
+
return(w)
}
--
GitLab