# An R package for proteomics data quality control

## Documentation for package ‘proteoQC’ version 1.4.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## 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