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proteoQC (version 1.4.0)

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

1.4.0

License

LGPL-2

Maintainer

Bo Wen

Last Published

February 15th, 2017

Functions in proteoQC (1.4.0)

getMods

Get the modification list

labelRatio

Calculate the labeling efficiency of isobaric labeling data

addSummaryChart

Add PRIDE summary charts

getEnzyme

Get the enzymes list

createTargetDecoyDB

Create target-decoy database

loadmsQCres

Load the result of msQCpipe

combineRun

Combine multiple results

cntStat

contaminants stat

calcMSQCMetrics

Calculate the MS1 and MS2 level QC metrics

chargeStat

Charge distribution

msQCpipe

The main function of msQC pipeline

print.msQCres

Print the information of msQCres object

plotFractionIDResult

Barplot in different level for each fraction

plotMS2Error

plot MS2 mass error

plotSampleIDResultErrorBar

Error barplot in different level for each fraction

plotSampleVenn

Venn plot in sample level

plotMS1Error

plot MS1 mass error

plotBioRepVenn

Venn plot in biological replicate level

plotMS2Error_obsolete

plot MS2 mass error

plotTechRepVenn

Venn plot in technical replicate level

HTML format report generator

showMods

Shown all modifications