hmld {ldblock} | R Documentation

## 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

### 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

[Package ldblock version 1.22.1 Index]