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 1.4.0 Index]