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

Description Usage Arguments Value Examples

View source: R/VCFQAReport.R

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

1

Arguments

Object

an object of type VCFQAReport

Value

True or False if sample passed all thresholds

Examples

1
2
3
4
5
6
7
8
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)

Bioconductor-mirror/genotypeeval documentation built on June 1, 2017, 9:43 a.m.