genotypeeval (version 1.2.2)

didSamplePassOverall: Getter for VCFEvaluate class to check if Sample Passed. Using thresholds from VCFQAParam object return a list. First return whether each test was passed (TRUE) or failed (FALSE). Then return an overall pass (TRUE) or fail (FALSE).

Description

Getter for VCFEvaluate class to check if Sample Passed. Using thresholds from VCFQAParam object return a list. First return whether each test was passed (TRUE) or failed (FALSE). Then return an overall pass (TRUE) or fail (FALSE).

Usage

didSamplePassOverall(Object)

Arguments

Object

an object of type VCFQAReport

Value

• True or False if sample passed all thresholds

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)
didSamplePassOverall(ev)