| read_ped {BGLR} | R Documentation |
read_ped
Description
This function reads genotype information stored in PED format used in plink.
Usage
read_ped(ped_file)
Arguments
ped_file |
ASCII file with genotype information. |
Details
The PED file is a white-space (space or tab) delimited file: the first six columns are mandatory:
Family ID Individual ID Paternal ID Maternal ID Sex (1=male; 2=female; other=unknown) Phenotype
The IDs are alphanumeric: the combination of family and individual ID should uniquely identify a person. A PED file must have 1 and only 1 phenotype in the sixth column. The phenotype can be either a quantitative trait or an affection status column.
Value
The routine will return a vector of dimension n*p (n=number of individuals, p=number of snps), with the snps stacked.
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_ped)
## End(Not run)