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` | colour: 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

An object created by `ggplot`

### 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 1.8.2 Index]