subsetVCF: Generate a market subset of a vcf file

In adimitromanolakis/sim1000G: Genotype Simulations for Rare or Common Variants Using Haplotypes from 1000 Genomes

Description

Generate a market subset of a vcf file

Usage

subsetVCF(vcf, var_index = NA, var_id = NA, individual_id = NA)

Arguments

vcf	VCF data as created by function readVCF
var_index	index of number to subset. Should be in the range 1..length(vcf$varid)
var_id	id of markers to subset. Should be a selection from vcf$varid. NA if no filtering on id to be performed.
individual_id	IDs of individuals to subset. Should be a selection from vcf$individual_id

Value

VCF object to be used by startSimulation function.

Examples

examples_dir = system.file("examples", package = "sim1000G")

vcf_file = file.path(examples_dir, "region-chr4-93-TMEM156.vcf.gz")

vcf = readVCF( vcf_file, maxNumberOfVariants = 500 ,
               min_maf = 0.02 ,max_maf = NA)

vcf2 = subsetVCF(vcf, var_index = 1:50)

adimitromanolakis/sim1000G documentation built on Sept. 29, 2021, 3:44 a.m.