Read haplotype data, selected by region of interest, from BED files (regular PLINK binary files)

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Description

Read haplotype data, selected by region of interest, from BED files (regular PLINK binary files)

Usage

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read.haplo.bedfile(filename = "NULL", map, chr = "NULL",
  startpos = "NULL", endpos = "NULL")

Arguments

filename

character, path to BED file containing haplotype data. Attention! filename should contain path to <file>.bed with full file name. For example ../mydata/inputplink.bed.

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.shapeit_haps, readMapFile

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