ts_eigenstrat: Convert genotypes to the EIGENSTRAT file format

In bodkan/slendr: A Simulation Framework for Spatiotemporal Population Genetics

Convert genotypes to the EIGENSTRAT file format

Description

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

Usage

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

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).

Value

Object of the class EIGENSTRAT created by the admixr package

bodkan/slendr documentation built on Dec. 19, 2024, 11:41 p.m.