loadSNPDataFromVCF: loadSNPDataFromVCF
In CopyNumberPlots: Create Copy-Number Plots using karyoploteR functionality

Description Usage Arguments Details Value Examples

Load BAF-like data from a VCF file based on the variant allele frequency

1	loadSNPDataFromVCF(vcf.file, regions=NULL, genome="hg19", mirror.baf=TRUE, verbose=TRUE)

`vcf.file`	The name of the VCF file with the data
`regions`	The regions to which we will limit the import (defaults to NULL)
`genome`	(a character)The name of the genome (defaults to "hg19")
`mirror.baf`	Flip the baf of about half the snps (the ones in odd positions in the genome) to achieve a mirror-like effect as in SNP arrays (defaults to TRUE)
`verbose`	Wether information messages should be generated. (defaults to TRUE)

Given a VCF file the function will compute BAF-like values based on the variant allele frequency contained in it and return a GRanges object with a column named "baf".

A GRanges object with a range per variant and a column named baf

vcf.file <- system.file("extdata", "example.vcf.gz", package = "CopyNumberPlots", mustWork = TRUE)
# These examples fail in windows. Commenting them out temporarily
# snps <- loadSNPDataFromVCF(vcf.file)

#kp <- plotKaryotype(plot.type = 4)
#plotBAF(kp, snps = snps, labels = names(snps))