GWAS entries in CHANGELOG and documentation

[NeuKon]

Hi @covaruber,

Thank you very much for your work on this amazing package.

The CHANGELOG mentions the following under ## PENDINGS AND PRIORITIES: 1) enable P3D argument

• The GWAS documnentation does already mention the use of P3D=TRUE/FALSE. Does this argument currently have no effect? If so, what is the current behaviour?

2) Enable GWAS for unimputed markers?

• I am not sure how much development effort this would be. mmer can handle missing data, so a current workaround would be to fit individual mmer models with unimputed markers as the explanatory variable. This is clearly impractical for big datasets. Some quick tests suggest there is more to it then simply removing the few lines of code in GWAS that check for missing data.

In addition, the GWAS documentation suggests the marker matrix M must be encoded as -1,0,1. In general, mmer and thus GWAS should be able to cope with different SNP values (e.g. 0,1,2,3,4 for tetraploids or ratio values [0, 1] for alternative alleles over total read depth), at least for additive models? Perhaps this is just an issue for some "convenience" features like MAF checks etc? In this case only small changes might be required (e.g. a warning if marker values are anything else than -1,0,1.

Best wishes, Konrad

EDIT: Rephrased the last point about marker encoding

[covaruber]

Konrad, thanks a lot for the feedback. I will work on the documentation. Indeed, can be misleading. Currently, the current behavior is that P3D=TRUE, of course P3D=FALSE would be estimating one marker at the time. The reason why is not enabled is more due to the way currently I am using the Rcpp code. The current Rcpp implementation for P3D=TRUE fits the emmer model, extracts the VCs and does the for loop for each marker in Rcpp. I just haven't had the time to code the for loop for P3D=FALSE. Mostly for having other priorities (the mmec() function and rebuilding mmer()) but feel free to code it and send a pull request :) otherwise I may do it in this quarter.

The coding part is a great suggestion, I should rewrite the documentation. I'll do that right away. Thanks.

Cheers, Eduardo

[covaruber]

P3D enabled and pushed to GitHub, to be tested now.

Cheers, Eduardo