ReadVCFData {genotypeeval} | R Documentation |
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.
ReadVCFData(mydir, myfile, genome)
mydir |
Directory of vcf file |
myfile |
Filename of vcf file |
genome |
GRCh37 or GRCh38 |
Object of class VCFData
vcffn <- system.file("ext-data", "chr22.GRCh38.vcf.gz", package="genotypeeval") mydir <- paste(dirname(vcffn), "/", sep="") myfile <-basename(vcffn) vcf <- ReadVCFData(mydir, myfile, "GRCh38")