read.haplo.pedfile: Read haplotype data, selected by region of interest, from PED...

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

Description

Read haplotype data, selected by region of interest, from PED files (regular PLINK untransposed text files)

Usage

read.haplo.pedfile(filename = "NULL", map, chr = "NULL",
  startpos = "NULL", endpos = "NULL")

Arguments

filename	character, path to PED file containing haplotype data. Attention! filename should contain path to <file>.ped with full file name. For example ../mydata/inputplink.ped
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.bedfile, read.haplo.shapeit_haps, readMapFile

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