Understanding MiDAS Analysis Results Table for N(disease=1) [%] Column

[mattkrantz]

Hi there, thanks so much for the work on the midasHLA package.

I had a question about understanding the results of the "N(disease=1) [%]" column from the following table from the tutorial (https://genentech.github.io/midasHLA/articles/MiDAS_tutorial.html#hla-association-analysis), which has 500 cases and 500 controls in the tutorial data.

`HLA_results_cond <- runMiDAS(
object = HLA_model,
experiment = "hla_alleles",
inheritance_model = "dominant",
conditional = TRUE,
lower_frequency_cutoff = 0.02,
upper_frequency_cutoff = 0.98,
correction = "bonferroni",
exponentiate = TRUE
)

kableResults(HLA_results_cond, scroll_box_height = "200px")`

For the first row of output, assuming a dominant inheritance model, if the N of disease individuals is 129 that carry one or more DQB1*06:02 risk allele, shouldn't the N(disease=1) [%] be equal to 25.8% (129/500) instead of 12.9%.

[mcjmigdal]

Hi, it looks like we calculated it as 129 / 500 cases and 500 controls = 12.9%.

[mattkrantz]

Thanks! So then do you think to get the correct N(disease=1) and N(disease=0) %, I should multiply those columns by 2 assuming the dominant inheritance model? Thanks so much!