Read haplotype data, selected by region of interest, from a .haps file (regular ShapeIt output files)

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Description

Read haplotype data, selected by region of interest, from a .haps file (regular ShapeIt output files)

Usage

1
read.haplo.shapeit_haps(filename, map, chr, startpos, endpos)

Arguments

filename

character, path to a .haps file containing haplotype data which is regular ShapeIt output. See https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html#hapsample

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.pedfile, read.haplo.bedfile, readMapFile

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