ldtagr {gwascat} | R Documentation

## 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

### Details

uses snpStats ld()

### Value

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

### Note

slow but safe approach. probably a matrix method could be substituted using the nice sparse approach already in snpStats

### Author(s)

VJ Carey

### Examples

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

[Package gwascat version 2.16.1 Index]