TargetExperiment-plotRegion: Plot read profiles for a particular genomic region.

In gamerino/TarSeqQC: TARgeted SEQuencing Experiment Quality Control

Description

plotRegion plots the read profiles for a selected region. The minAAF parameter set the minimum proportion value to call an SNP and the minRD the minimum read depth. They are combined to obtain a minimum read count value at each position used to distinguish between possible SNPs and background noise. If SNPs is set as 'TRUE', colored bars will appear indicating the occurrence of possible SNPs surpassing the minAAF and minRD, at each genomic position.

Usage

plotRegion(object, region, seqname, SNPs = TRUE, minAAF=0.05, minRD=10, 
    xlab = "", title = "", size = 0.5, BPPARAM = bpparam())

## S4 method for signature 'TargetExperiment'
plotRegion(object, region, seqname, SNPs = TRUE,
    minAAF=0.05, minRD=10, xlab = "", title = "", size = 0.5, 
    BPPARAM = bpparam())

Arguments

object	TargetExperiment object.
region	Numeric of length two indicating the selected genomic region.
seqname	Character indicating the chromosome of the genomic region.
SNPs	Logical flag indicating if SNPs should be plotted.
minAAF	Numeric indicating the minimum alternative allele proportion necessary to call a SNP.
minRD	Numeric indicating the minimum read depth of alternative alleles necessary to call a SNP.
xlab	Character containing the axis x label.
title	Character containing the plot title.
size	Numeric indicating the size of line plots.
BPPARAM	An optional BiocParallelParam instance defining the parallel back-end to be used during evaluation.

Value

ggplot2 graphics.

include TargetExperiment-FeatPerform.R

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)

# getting and exploring a sequenced region of a particular gene
getRegion(ampliPanel, level="gene", ID="gene7", collapse=FALSE)
# plot a particular genomic region
g<-plotRegion(ampliPanel,region=c(4500,6800), seqname="chr10", SNPs=TRUE,  
xlab="", title="gene7 amplicons",size=0.5)
# x11(type="cairo")
if(interactive()){
g
}

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