Question submitted via email: "I was wondering how X chromosome association analyses are performed by GENESIS, in particular, how are males coded and analyzed?"

The answer to this question depends on how your input data is formatted, but the most common format is to code males as diploid, with X chromosome variants assigned a dosage of 2 for males. assocTestSingle has an argument male.diploid which defaults to TRUE, but can be changed if your data file codes males as haploid.

When male.diploid=TRUE, the allele frequencies reported by GENESIS will adjust allele counts for males on the X chromosome, so that males contribute half as much as females when counting alleles. For this correction to be made, the SeqVarData object must contain a sex column in its sampleData AnnotatedDataFrame.