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

Description Usage Arguments Value Examples

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

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didSamplePass(Object)

Arguments

Object

an object of type VCFQAReport

Value

Vector of True and False

Examples

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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.