Question submitted via email: Is there a simple way to get around the default human genome assumption in GENESIS? I can recode my bovine genotype data so that the autosome number is reduced to 22 as in human, but I'm hoping there is a simpler solution.

If you are using GWASTools to set up your data objects in GENESIS, see the man page for the GenotypeData class for an example of how to create a GenotypeData object for a non-human organism. You have to specify the chromosome codes that correspond to the autosomes and sex chromosomes in your organism.

In the pcair function, you can pass additional arguments that will be interpreted by SNPRelate::snpgdsPCA, which is the underlying function used to calculate principal components. In this case you could set autosome.only=FALSE to use all chromosomes (as the default is to use chromosomes 1:22), or autosome.only=1:N where Nis the number of autosomes in your organism.