Hello,

A colleague of mine brought to my attention that two GENESIS functions, fitNullMM() and assocTestMM() have become defunct in the latest version of GENESIS; and have been replaced by fitNullModel() and assocTestSingle(). I am now trying to work on modifying a crop GWAS pipeline that uses these defunct functions so that these new functions are incorporated. However, I am hitting a wall because of data formatting issues (for the genotype files) required for assocTestSingle().

I would report error message that I am getting, but I am not receiving any error messages. Instead, the object I am getting form assocTestSingle(iterator, nullmod, test = "Score") is empty (0 rows, and 9 columns).

I have deduced that the source of the error is likely from the formatting of the genotype file. That is, assocTestSingle() seems accept an object created by GenotypeBlockIterator() instead of an object created from GenotypeData() (and assocTestMM() ran fine for an object from GenotypeData). Therefore, my uneducated guess is that GenotypeBlockIterator() is not reading my data from GenotypeData().

Could I please trouble you to 30 minutes of your time over the next week or two for assistance with troubleshooting the formatting issues I am running into?

Thank you for your time.

Alex