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

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

## S4 method for signature 'TargetExperiment'
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

Note

see full example in TargetExperiment-class

Author(s)

Gabriela A. Merino gmerino@bdmg.com.ar, Cristobal Fresno cfresno@bdmg.com.ar, Yanina Murua ymurua@leloir.org.ar, Andrea S. Llera allera@leloir.org.ar and Elmer A. Fernandez efernandez@bdmg.com.ar

See Also

plotFeature

Examples

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## 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")
if(interactive()){
g
}

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