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.
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:
ll{
Integer code Genotype
0 00 Homozygote "1"/"1"
1 01 Heterozygote
2 10 Missing genotype
3 11 Homozygote "2"/"2"
}
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.