loadSNPDataFromVCF: loadSNPDataFromVCF

In bernatgel/CopyNumberPlots: Create Copy-Number Plots using karyoploteR functionality

loadSNPDataFromVCF

Description

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

Usage

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

Arguments

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)

Details

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".

Value

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

Examples

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))

bernatgel/CopyNumberPlots documentation built on Sept. 22, 2023, 1:53 a.m.