TarSeqQC (version 1.2.0)

plotNtdPercentage: Plot nucleotide read percentages for a particular feature.

Description

plotNtdPercentage plots the percentages of the ocurrence of each nucleotide in each position for a selected feature.

Usage

plotNtdPercentage(object, featureID, BPPARAM = bpparam())
"plotNtdPercentage"(object, featureID, BPPARAM = bpparam())

Arguments

object

a TargetExperiment object.

featureID

a character indicating the feature ID.

BPPARAM

An optional BiocParallelParam instance defining the parallel back-end to be used during evaluation.

returned by the function.

Value

ggplot2 graphics

See Also

plotFeature

Examples

if(interactive()){
## loading TargetExperiment object
data(ampliPanel, package="TarSeqQC")
## Defining bam file, bed file and fasta file names and paths
setBamFile(ampliPanel)<-system.file("extdata", "mybam.bam",
    package="TarSeqQC", mustWork=TRUE)
setFastaFile(ampliPanel)<-system.file("extdata", "myfasta.fa",
    package="TarSeqQC", mustWork=TRUE)
# Exploring the nucleotide percentages compositions of the read counts for a
# particular amplicon
g<-plotNtdPercentage(ampliPanel,featureID="AMPL20")
g
}