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

Description Usage Arguments Details Value Note Author(s) Examples

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

1	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` 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

uses snpStats ld()

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

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