didSamplePass: Getter for VCFEvaluate class to check if Sample Passed....

In jentom/genotypeeval: QA/QC of a gVCF or VCF file

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

didSamplePass(Object)

Arguments

Object

an object of type VCFQAReport

Value

Vector of True and False

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)
didSamplePass(ev)

jentom/genotypeeval documentation built on May 13, 2019, 12:54 p.m.