hmld {ldblock}R Documentation

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

Details

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

Value

instance of ldstruct class

Examples

getClass("ldstruct")
# see vignette

[Package ldblock version 1.12.1 Index]