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

Description Usage Arguments Value See Also

View source: R/read.haplo.R

Description

Read haplotype data, selected by region of interest, from PLINK formatted files or ShapeIt output files

Usage

1
2
read.haplo(type = "bed", filename, map, chr = 0, startpos = 0,
  endpos = 0)

Arguments

type

character, 'ped', 'bed' (default) or 'shapeit-haps' format of input file containing haplotype data

filename

character, path to input file containing haplotype data

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


RVPedigree documentation built on May 19, 2017, 8:55 p.m.

Search within the RVPedigree package
Search all R packages, documentation and source code