[BioC] SKAT package on CRAN

[Cian Murphy]

I'm attempting to run SKAT for the gene based tests. For the null model section, the code is:

obj <-SKAT_Null_Model(phenotype ~ covariates_matrix, out_type="D")

where phenotype is a numeric binary of 0/1 for case/control status. Does it matter if 0 is case or control and vice  versa?

Secondly, how exactly do you get the covariates matrix? For gene based tests, what are the covariates? If all I have is patient ID, case/control status and genotype data (0/1/2 or NA), how should I set this up?

Thanks,

Cian