read.haplo.shapeit_haps: Read haplotype data, selected by region of interest, from a...

In RVPedigree: Methods for Family-Based Rare-Variant Genetic Association Tests

Description

Read haplotype data, selected by region of interest, from a .haps file (regular ShapeIt output files)

Usage

read.haplo.shapeit_haps(filename, map, chr, startpos, endpos)

Arguments

filename	character, path to a .haps file containing haplotype data which is regular ShapeIt output. See https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html#hapsample
map	object, data.frame contains 3 columns: rsID, chromosome, position in bp as output by e.g. readMapFile.
chr	character, chromosome number (basically from 1 to 22 as used by Plink), on which the region of interest is located
startpos	numeric, start position (in bp, base pairs) of the region of interest (default: 0)
endpos	numeric, end position (in bp, base pairs) of the region of interest (default: 0)

Value

matrix object containing the haplotypes selected by the region of interest

See Also

read.haplo, read.haplo.pedfile, read.haplo.bedfile, readMapFile

RVPedigree documentation built on May 29, 2017, 10:19 p.m.