EIGENSTRAT data produced by this function can be used by the admixr R package (https://bodkan.net/admixr).

ts_eigenstrat(ts, prefix, chrom = "chr1", outgroup = NULL)

Arguments

ts

pyslim.SlimTreeSequence object

prefix

EIGENSTRAT trio prefix

chrom

The name of the chromosome in the EIGENSTRAT snp file (default "chr1")

outgroup

Should a formal, artificial outgroup be added? If NULL (default), no outgroup is added. A non-NULL character name will serve as the name of the outgroup in an ind file.

Value

Object of the class EIGENSTRAT created by the admixr package

Details

In case an outgroup was not formally specified in a slendr model which generated the tree sequence data, it is possible to artificially create an outgroup sample with the name specified by the outgroup argument, which will carry all ancestral alleles (i.e. value "2" in a geno file for each position in a snp file).