read.haplo.bedfile: Read haplotype data, selected by region of interest, from BED files (regular PLINK binary files)

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


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

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