ldtagr: expand a list of variants by including those in a VCF with LD...
In gwascat: representing and modeling data in the EMBL-EBI GWAS catalog

Description Usage Arguments Value Note Author(s) Examples

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

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

`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

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

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

VJ Carey

 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)