gwascat (version 2.4.2)

ldtagr: expand a list of variants by including those in a VCF with LD exceeding some threshold

Description

expand a list of variants by including those in a VCF with LD exceeding some threshold

Usage

ldtagr(snprng, tf, samples, genome = "hg19", lbmaf = 0.05, lbR2 = 0.8, radius = 1e+05)

Arguments

snprng

a named GRanges for a single SNP. The name must correspond to the name that will be assigned by genotypeToSnpMatrix to the corresponding column of a SnpMatrix.

tf

TabixFile instance pointing to a bgzipped tabix-indexed VCF file

samples

a vector of sample identifiers, if excluded, all samples used

genome

tag like 'hg19'

lbmaf

lower bound on variant MAF to allow consideration

lbR2

lower bound on R squared for regarding SNP to be incorporated

radius

radius of search in bp around the input range

Value

• a GRanges with names corresponding to 'new' variants and mcols fields 'paramRangeID' (base variant input) and 'R2'

Details

uses snpStats ld()

Examples

require(GenomicRanges)
cand = GRanges("1", IRanges(113038694, width=1))
names(cand) = "rs883593"
require(VariantAnnotation)
expath = dir(system.file("vcf", package="GGtools"), patt=".*exon.*gz$", full=TRUE)
tf = TabixFile(expath)
ldtagr( cand, tf, lbR2 = .8)
# should do with 1000 genomes in S3 bucket and gwascat