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

Description

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

Usage

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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


Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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