Description Usage Arguments Value Author(s) Examples
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://pngu.mgh.harvard.edu/~purcell/plink/binary.shtml.
1 | read_bed(bed_file,bim_file,fam_file,na.strings,verbose)
|
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. |
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" |
Gustavo de los Campos, Paulino Perez Rodriguez,
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