coveragePlot {qPLEXanalyzer}R Documentation

Plot peptide sequence coverage

Description

Computes and displays peptide sequence coverage in proteomics experiment

Usage

coveragePlot(MSnSetObj, ProteinID, ProteinName, fastaFile, myCol="brown")

Arguments

MSnSetObj

MSnSet: an object of class MSnSet

ProteinID

character: Uniprot ID of the protein

ProteinName

character: name of the protein

fastaFile

character: fasta file of protein sequence

myCol

character: colour for plotting

Details

In the qPLEX-RIME experiment it is imperative for bait protein to have good sequence coverage. This function plots the protein sequence coverage of the bait protein in the qPLEX-RIME experiment. It requires the fasta sequence file of bait protein as input to generate the plot.

Value

A protein coverage plot of selected protein for quantitative proteomics data.

Examples

data(human_anno)
data(exp3_OHT_ESR1)
MSnSet_data <- convertToMSnset(exp3_OHT_ESR1$intensities_qPLEX1, metadata=exp3_OHT_ESR1$metadata_qPLEX1,
indExpData=c(7:16), Sequences=2, Accessions=6)
mySequenceFile <- system.file('extdata', "P03372.fasta", package="qPLEXanalyzer")
coveragePlot(MSnSet_data, ProteinID="P03372", ProteinName="ERa", fastaFile=mySequenceFile)

[Package qPLEXanalyzer version 1.0.4 Index]