ldblock (version 1.2.2)

hmld: import hapmap LD data and create a structure for its management

Description

import hapmap LD data and create a structure for its management

Usage

hmld(hmgztxt, poptag, chrom, genome = "hg19", stat = "Dprime")

Arguments

hmgztxt

name of gzipped text file as distributed at hapmap.ncbi.nlm.nih.gov/downloads/ld_data/2009-02_phaseIII_r2/. It will be processed by read.delim.

poptag

heuristic tag identifying population

chrom

heuristic tag for chromosome name

genome

genome tag

stat

statistic to use, "Dprime", "R2", and "LOD" are options

Value

• instance of ldstruct class

Details

generates a sparse matrix representation of pairwise LD statistics and binds metadata on variant name and position

Examples

getClass("ldstruct")
# see vignette