A parser for Mascot search results ( both PMF and MSMS) in R package.
install.packages("devtools")
library("devtools")
install_github("mascotParser","nghiavtr")
library("mascotParser")
library(MascotParser)
filename <- "MSMS_Mascot_search_result.dat";
myParse <- parse(new("MascotParser"),filename)
myParse@qexp
myParse@qintensity
myParse@MSMSnumQuery
myParse@PIHnumHits
myParse@PIHhitScores
myms2=getMSMSqueryInfo(myParse,3)
myms2$mz
myms2$intensity
plotSpec(myParse,specTitle=NULL,queryId=NULL)
plotSpec(myParse,specTitle=NULL,queryId=1)
mz1=getMSMSqueryInfo(myParse,1)$mz
int1=getMSMSqueryInfo(myParse,1)$intensity
mz2=getMSMSqueryInfo(myParse,2)$mz
int2=getMSMSqueryInfo(myParse,2)$intensity
plotSpecPanel(mz1,int1,mz2,int2,xlimVal=500,plotTitle="test title")
library(MascotParser)
filename <- "PMF_Mascot_search_result.dat";
myParse <- parse(new("MascotParser"),filename)
negPeaks <- myParse@qexp[getUnassignedPeaks(myParse, scoreThres=MascotThres)]
plotSpec(myParse,specTitle=NULL,queryId=NULL)
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