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proteoQC (version 1.8.2)

An R package for proteomics data quality control

Description

This package creates a HTML format QC report for MS/MS-based proteomics data. The report is intended to allow the user to quickly assess the quality of proteomics data.

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Version

Version

1.8.2

License

LGPL-2

Maintainer

Bo Wen

Last Published

February 15th, 2017

Functions in proteoQC (1.8.2)

calcMSQCMetrics

Calculate the MS1 and MS2 level QC metrics
plotMS1Error

plot MS1 mass error
labelRatio

Calculate the labeling efficiency of isobaric labeling data
plotBioRepVenn

Venn plot in biological replicate level
cntStat

contaminants stat
runTandem

Run X!Tandem
plotMS2Error

plot MS2 mass error
showMods

Shown all modifications
showEnzyme

Shown all enzymes
plotFractionIDResult

Barplot in different level for each fraction
plotTechRepVenn

Venn plot in technical replicate level
plotSampleVenn

Venn plot in sample level
addSummaryChart

Add PRIDE summary charts
combineRun

Combine multiple results
loadmsQCres

Load the result of msQCpipe
createTargetDecoyDB

Create target-decoy database
getMods

Get the modification list
msQCpipe

The main function of msQC pipeline
getEnzyme

Get the enzymes list
proteinGroup

Protein inference
chargeStat

Charge distribution
plotSampleIDResultErrorBar

Error barplot in different level for each fraction
reportHTML

HTML format report generator
plotMS2Error_obsolete

plot MS2 mass error
print.msQCres

Print the information of msQCres object