From 50077a7e0618303d41fc7d0d25dd76907362672b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Todor=20Kondi=C4=87?= <todor.kondic@uni.lu>
Date: Sun, 17 May 2020 06:15:07 +0200
Subject: [PATCH] extraction: remove id detection from mz columns
* extraction.R(gen_mz_range,gen_rt_range): Updated. Rownames are not
IDs anymore.
(gen_ms1_chrom): Updated.
---
R/extraction.R | 17 +++++++----------
1 file changed, 7 insertions(+), 10 deletions(-)
diff --git a/R/extraction.R b/R/extraction.R
index 0fcd989..ccbf4d5 100644
--- a/R/extraction.R
+++ b/R/extraction.R
@@ -57,17 +57,15 @@ id2name<-function(id) {paste("ID:",id,sep='')}
ppm2dev<-function(m,ppm) 1e-6*ppm*m
-
-
gen_mz_range<-function(mz,err) {
- mat<-matrix(data=numeric(1),nrow=length(mz),ncol=2,dimnames=list(as.character(names(mz))))
+ mat<-matrix(data=numeric(1),nrow=length(mz),ncol=2)
mat[,1]<-mz - err
mat[,2]<-mz + err
mat
}
gen_rt_range<-function(rt,err) {
- mat<-matrix(data=numeric(1),nrow=length(rt),ncol=2,dimnames=list(as.character(names(rt))))
+ mat<-matrix(data=numeric(1),nrow=length(rt),ncol=2)
rV<-which(!is.na(rt))
rNA<-which(is.na(rt))
mat[rV,1]<-(rt[rV] - err)*60
@@ -265,19 +263,18 @@ gen_ms2_chrom<-function(ms2Spec) {
}
-gen_ms1_chrom<-function(raw,mz,errEIC,rt=NULL,errRT=NULL) {
- mzRng<-gen_mz_range(mz,err=errEIC)
- rtRng<-gen_rt_range(rt,err=errRT)
- ids<-dimnames(mzRng)[[1]]
+gen_ms1_chrom <- function(raw,mz,errEIC,id,rt=NULL,errRT=NULL) {
+ mzRng<-gen_mz_range(mz,err = errEIC)
+ rtRng<-gen_rt_range(rt,err = errRT)
x<-MSnbase::chromatogram(raw,mz=mzRng,msLevel=1,missing=0.0,rt=rtRng)
res<-lapply(x,function (xx) {
rt<-MSnbase::rtime(xx)/60.
ints<-MSnbase::intensity(xx)
- df<-data.frame(rt=rt,intensity=ints,stringsAsFactors=F)
+ df<-dtable(rt=rt,intensity=ints)
df
})
- names(res)<-ids
+ names(res)<-id
res
}
--
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