plotRegion {TarSeqQC} | R Documentation |
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.
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())
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. |
ggplot2 graphics.
include TargetExperiment-FeatPerform.R
see full example in TargetExperiment-class
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
## 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 }