BGLR (version 1.0.4)

read_ped: 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.

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"

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.

Examples

## Not run: 
# 
# library(BGLR)
# demo(read_ped)
# 
# ## End(Not run)