coveragePlot: Plot peptide sequence coverage

In crukci-bioinformatics/qPLEXanalyzer: Tools for quantitative proteomics data analysis

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)

crukci-bioinformatics/qPLEXanalyzer documentation built on Sept. 24, 2024, 1:13 a.m.