convert.vcf: convert .vcf files to MatrixEQTL genotype input

In matthiasheinig/eQTLpipeline: A package to facilitate the full pipeline of cis eQTL analysis

Description

convenience function to convert genotypes from .vcf files to the MatrixEQTL format

Usage

convert.vcf(vcf.file, which = "GT", map = FALSE, snp.pos = FALSE,
  genotype_file_name = NULL)

Arguments

vcf.file	vcf.file containing genotypes
which	which field of the .vcf file to use: "GT" = genotype, "DS" = genotype dosage from MaCH/Thunder, "GL" = genotype likelihoods (default "GT")
map	should the map object extracted from
snp.pos	names for colums with annotations for custom build, order: chromosome (chr), length (pos) (default NULL)
genotype_file_name

Value

either a matrix nsnps x nsample containing genotypes coded as 0,1,2 or a list with slots "gt.mat", "map", "snp.pos"

Author(s)

Ines Assum (2019-03-21)

matthiasheinig/eQTLpipeline documentation built on May 21, 2019, 1:16 p.m.