didSamplePass {genotypeeval} | R Documentation |
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).
didSamplePass(Object)
Object |
an object of type VCFQAReport |
Vector of True and False
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)