read_bed {BGLR}

read_bed

Description

This function reads genotype information stored in binary PED (BED) files used in plink. These files save space and time. The pedigree/phenotype information is stored in a separate file (*.fam) and the map information is stored in an extededed MAP file (*.bim) that contains information about the allele names, which would otherwise be lost in the BED file. More details http://zzz.bwh.harvard.edu/plink/binary.shtml.

Usage

  read_bed(bed_file,bim_file,fam_file,na.strings,verbose)

Arguments

bed_file

binary file with genotype information.

bim_file

text file with pedigree/phenotype information.

fam_file

text file with extended map information.

na.strings

missing value indicators, default=c("0","-9").

verbose

logical, if true print hex dump of bed file.

Value

The routine will return a vector of dimension n*p (n=number of individuals, p=number of snps), with the snps(individuals) stacked, depending whether the BED file is in SNP-major or individual-major mode.

The vector contains integer codes:

Integer code	Genotype
0	00 Homozygote "1"/"1"
1	01 Heterozygote
2	10 Missing genotype
3	11 Homozygote "2"/"2"

Author(s)

Gustavo de los Campos, Paulino Perez Rodriguez,

Examples

## Not run: 

library(BGLR)
demo(read_bed)


## End(Not run)