genotypeeval (version 1.2.2)

getPlots: Getter for VCFQAReport class to return plots slot.

Description

Getter for VCFQAReport class to return plots slot.

Usage

getPlots(Object)

Arguments

Object

Object of Class VCFQAReport

Value

• List of named ggplots

Examples

vcffn <- system.file("ext-data", "chr22.GRCh38.vcf.gz", package="genotypeeval")
mydir <- paste(dirname(vcffn), "/", sep="")
myfile <-basename(vcffn)
svp <- ScanVcfParam(which=GRanges("22", IRanges(0,200e5)), geno="GT")
vcfparams <- VCFQAParam(count.limits=c(3014580000, Inf), readdepth.target = 30)
vcf <- ReadVCFData(mydir, myfile, "GRCh38")
ev <- VCFEvaluate(vcf, vcfparams)
getPlots(ev)