No covariates and effect allele documentation

[aarizvi]

"We recently conducted a GWAS using your gwasurvivr package (thank you!) and were wondering if it is possible to run the analysis without covariate adjustment (the function insists on receiving an nonempty character vector of covariates). If so, can you please advise us on how to do so?"

"On a related note, can you please clarify which allele is being modeled as the effect allele in the output file and which column contains the frequency of the effect allele in the sample? We can’t seem to find this in the documentation or supplementary documentation.

For example, AF is generally equal to MAF, and SAMP_FREQ_ALT is generally equal to SAMP_MAF. But MAF and SAMP_MAF are not equal to each other."

[chico836]

Had this issue been resolved. I have a similar question regarding running without covariates. Thank you

[shirleydaidai]

Same problem here. Even run the example code for interaction analysis. "Error in inter.term %in% covariates: cannot find 'covariates'"

[PoojaMiddha]

I have the same question. Which allele does the package gives HR for if one is not using flip.dosage=TRUE in their script?