TarSeqQC (version 1.2.0)

plotRegion: Plot read profiles for a particular genomic region.

Description

plotRegion plots the read profiles for a selected region. If SNPs is set as 'TRUE', colored bars will appear indicating the ocurrence of SNPs at each genomic position.

Usage

plotRegion(object, region, seqname, SNPs = TRUE, xlab = "", title = "", size = 0.5, BPPARAM = bpparam())
"plotRegion"(object, region, seqname, SNPs = TRUE, 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.

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

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)

# 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")
g
}