TargetExperiment-plotNtdPercentage: Plot nucleotide read percentages for a particular feature.

In gamerino/TarSeqQC: TARgeted SEQuencing Experiment Quality Control

Description

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

Usage

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 [e-mail], Cristobal Fresno [e-mail], Yanina Murua [e-mail], Andrea S. Llera [e-mail] and Elmer A. Fernandez [e-mail]

See Also

plotFeature

Examples

## 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
}

gamerino/TarSeqQC documentation built on Feb. 3, 2020, 9:19 p.m.