ReadVCFData: User Constructor for class. Calls VCFData constructor:...

Description Usage Arguments Value Examples

View source: R/VCFData.R

Description

User Constructor for class. Calls VCFData constructor: ReadVCFData is a wrapper for readVcfAsVRanges. It removes indels, GL chromosomes, and MULTI calls. It scans the header of the vcf file and adds in the following fields for analysis if present: AD, GT, DP, GQ. Looks for the "END" tag in the header and reads in file as gVCF if necessary.

Usage

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ReadVCFData(mydir, myfile, genome)

Arguments

mydir

Directory of vcf file

myfile

Filename of vcf file

genome

GRCh37 or GRCh38

Value

Object of class VCFData

Examples

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vcffn <- system.file("ext-data", "chr22.GRCh38.vcf.gz", package="genotypeeval")
mydir <- paste(dirname(vcffn), "/", sep="")
myfile <-basename(vcffn)
vcf <- ReadVCFData(mydir, myfile, "GRCh38")

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