coveragePlot {qPLEXanalyzer} | R Documentation |
Computes and displays peptide sequence coverage in proteomics experiment
coveragePlot(MSnSetObj, ProteinID, ProteinName, fastaFile, myCol = "brown")
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 |
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.
An object created by ggplot
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)