EIGENSTRAT data produced by this function can be used by the admixr R package (https://bodkan.net/admixr/).
Arguments
- ts
Tree sequence object of the class
slendr_ts- 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.
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).