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

In GreenwoodLab/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", recode = "recodeLetters")

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)
recode	character, designates if data are in 1/2 format or in letters (A, C, G, T) format. The defaut is 1/2 where 1 designating the minor allele

Value

matrix object containing the haplotypes selected by the region of interest, or NULL if there are no variants in the region

Author(s)

Lennart C. Karssen

Sodbo Sharapov

Karim Oualkacha

See Also

read.haplo, read.haplo.bedfile, read.haplo.shapeit_haps, readMapFile

GreenwoodLab/RVPedigree documentation built on May 6, 2019, 6:33 p.m.