ldByGene: Obtain LD statistics in region specified by a gene model.

In vjcitn/ldblock: data structures for linkage disequilibrium measures in populations

Description

Obtain LD statistics in region specified by a gene model.

Usage

ldByGene(sym = "MMP24", vcf = system.file("vcf/c20exch.vcf.gz", package
  = "gQTLstats"), flank = 1000, vcfSLS = "NCBI", genomeSLS = "hg19",
  stats = "D.prime", depth = 10)

Arguments

sym	A standard gene symbol for use with genemodel
vcf	Path to a tabix-indexed VCF file
flank	number of basepairs to flank gene model for search
vcfSLS	seqlevelsStyle (SLS) token for VCF; will be imposed on gene model
genomeSLS	character tag for genome, to be used with readVcf
stats	passed to ld
depth	passed to ld

Value

sparse matrix representation of selected LD statistic, as returned by ld

Note

Uses an internal function genemod4ldblock, that relies on EnsDb.Hsapiens.v75 to get gene model.

Examples

ld1 = ldByGene(depth=150)
image(ld1[1:200,1:200], col.reg=heat.colors(120), colorkey=TRUE,
 main="SNPs in MMP24 (chr20)") 

vjcitn/ldblock documentation built on Aug. 21, 2019, 8:50 p.m.