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

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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

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