ped: 'ped' format description

In LEA: LEA: an R package for Landscape and Ecological Association Studies

Description

Description of the ped format. The ped format can be used as an input format for genotypic matrices in the functions snmf, lfmm, and pca.

Details

The ped format has one row for each individual. Each row contains 6 columns of information for each individual, plus two genotype columns for each SNP. Each column must be separated by spaces or tabulations. The genotype format must be either 0ACGT or 01234, where 0 means missing genotype. The first 6 columns of the genotype file are: the 1st column is the family ID, the 2nd column is the sample ID, the 3rd and 4th columns are the sample IDs of parents, the 5th column is the gender (male is 1, female is 2), the 6th column is the case/control status (1 is control, 2 is case), the quantitative trait value or the population group label.

The ped format is described here.

Here is an example with 3 individuals and 4 SNPs:

1    SAMPLE0 0 0 2 2 1 2 3 3 1 1 2 1
2    SAMPLE1 0 0 1 2 2 1 1 3 0 4 1 1
3    SAMPLE2 0 0 2 1 2 2 3 3 1 4 1 2

Author(s)

Eric Frichot

See Also

ped2lfmm ped2geno geno lfmm.data ancestrymap vcf

LEA documentation built on Nov. 8, 2020, 8:19 p.m.