An R package for proteomics data quality control


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Documentation for package ‘proteoQC’ version 1.18.1

Help Pages

addSummaryChart Add PRIDE summary charts
calcMSQCMetrics Calculate the MS1 and MS2 level QC metrics
chargeStat Charge distribution
cntStat contaminants stat
combineRun Combine multiple results
createTargetDecoyDB Create target-decoy database
getEnzyme Get the enzymes list
getMods Get the modification list
labelRatio Calculate the labeling efficiency of isobaric labeling data
loadmsQCres Load the result of 'msQCpipe'
msQCpipe The main function of msQC pipeline
plotBioRepVenn Venn plot in biological replicate level
plotFractionIDResult Barplot in different level for each fraction
plotMS1Error plot MS1 mass error
plotMS2Error plot MS2 mass error
plotMS2Error_obsolete plot MS2 mass error
plotSampleIDResultErrorBar Error barplot in different level for each fraction
plotSampleVenn Venn plot in sample level
plotTechRepVenn Venn plot in technical replicate level
print.msQCres Print the information of msQCres object
proteinGroup Protein inference
reportHTML HTML format report generator
runTandem Run X!Tandem
showEnzyme Shown all enzymes
showMods Shown all modifications