From f545a07cd728414ad293c4a1d58855759a749636 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Todor=20Kondi=C4=87?= <todor.kondic@uni.lu>
Date: Wed, 2 Mar 2022 14:22:51 +0100
Subject: [PATCH] extraction: extract: Fix filterMz call
---
R/extraction.R | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/R/extraction.R b/R/extraction.R
index 82ec044..8093905 100644
--- a/R/extraction.R
+++ b/R/extraction.R
@@ -461,7 +461,7 @@ extr_msnb_ht <-function(file,wd,mz,errEIC, errFinePPM,errCoarse,fnSpec,rt=NULL,e
mzCrs<-gen_mz_range(mz=mz,err=errCoarse)
mzMin<-min(mzCrs)
mzMax<-max(mzCrs)
- ms1<-MSnbase::filterMz(ms1,c(mzMin,mzMax))
+ ms1<-MSnbase::trimMz(ms1,c(mzMin,mzMax))
fms2<-filt_ms2(ms1,ms2,mz,errCoarse=errCoarse,errFinePPM=errFinePPM)
## EICs for precursors.
@@ -522,7 +522,7 @@ extract <- function(fn,tag,tab,err_ms1_eic.,err_coarse,err_fine,err_rt.,missing_
mzmax <- max(mzrng)
read_ms1 <- function() {
ms1 <- MSnbase::readMSData(file=fn,msLevel=1,mode="onDisk")
- ms1 <- MSnbase::filterMz(ms1,c(mzmin,mzmax))
+ ms1 <- MSnbase::filterMz(ms1,mz=c(mzmin,mzmax),msLevel=1)
ms1
}
read_ms2 <- function() {
--
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