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.
read_bed(bed_file,bim_file,fam_file,na.strings,verbose)
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" |
binary file with genotype information.
text file with pedigree/phenotype information.
text file with extended map information.
missing value indicators, default=c("0","-9").
logical, if true print hex dump of bed file.
Gustavo de los Campos, Paulino Perez Rodriguez,
if (FALSE) {
library(BGLR)
demo(read_bed)
}
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