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

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

Description

import hapmap LD data and create a structure for its management; generates a sparse matrix representation of pairwise LD statistics and binds metadata on variant name and position

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

Examples

getClass("ldstruct")
# see vignette

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