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proteoQC (version 1.2.0)

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

1.2.0

License

LGPL-2

Maintainer

Bo Wen

Last Published

February 15th, 2017

Functions in proteoQC (1.2.0)

addSummaryChart

Add PRIDE summary charts

combineRun

Combine multiple results

loadmsQCres

Load the result of msQCpipe

labelRatio

Calculate the labeling efficiency of isobaric labeling data

Get the modification list

calcMSQCMetrics

Calculate the MS1 and MS2 level QC metrics

createTargetDecoyDB

Create target-decoy database

plotTechRepVenn

Venn plot in technical replicate level

msQCpipe

The main function of msQC pipeline

plotFractionIDResult

Barplot in different level for each fraction

plotBioRepVenn

Venn plot in biological replicate level

plotSampleIDResultErrorBar

Error barplot in different level for each fraction

plotMS1Error

plot MS1 mass error

plotSampleVenn

Venn plot in sample level

print.msQCres

Print the information of msQCres object

plotMS2Error_obsolete

Shown all modifications

reportHTML

HTML format report generator