lfmm: Input file for 'lfmm'

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

Description

Description of the lfmm format. The lfmm format can be used as an input format for genotypic matrices in the functions snmf, lfmm, lfmm2, and pca.

Details

The lfmm format has one row for each individual. Each row contains one value at each loci (separated by spaces or tabulations) corresponding to the number of alleles. The number of alleles corresponds to the number of reference alleles or the number of derived alleles. Missing genotypes are encoded by the value -9 or the value 9.

For the use of functions lfmm and lfmm2 missing genotypes must be removed or imputed with the function impute.

Here is an example of a genotypic matrix using the lfmm format with 3 individuals and 4 loci:

1 0 0 1
1 1 9 2
2 0 1 1

Author(s)

Eric Frichot

See Also

lfmm lfmm2 geno2lfmm lfmm2geno ancestrymap2lfmm ped2lfmm read.lfmm write.lfmm

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