ldtagr {gwascat} | R Documentation

## expand a list of variants by including those in a VCF with LD exceeding some threshold; uses snpStats ld()

### Description

expand a list of variants by including those in a VCF with LD exceeding some threshold; uses snpStats ld()

### 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 (from VariantTools) 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'

### 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

     cand = GenomicRanges::GRanges("1", IRanges::IRanges(113038694, width=1))
     names(cand) = "rs883593"
     requireNamespace("VariantAnnotation")
     expath = dir(system.file("vcf", package="gwascat"), patt=".*exon.*gz$", full=TRUE)
     tf = Rsamtools::TabixFile(expath)
     ldtagr( cand, tf, lbR2 = .8)

[Package gwascat version 2.22.0 Index]