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weizhouUMICH / SAIGE

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Missing --qCovarColList flag from step1_fitNULLGLMM.R wrapper script? #408

Open samuelejones opened 2 years ago

samuelejones commented 2 years ago

Following the steps in the SAIGE step 1 guide, I see that there is a --qCovarColList flag (complementing the main --covarColList flag) so that SAIGE knows which covariates are categorical and which are continuous.

Looking at the step1_fitNULLGLMM.R wrapper script (SAIGE v0.45), it seems that this flag doesn't exist, even though the fitNULLGLMM() function has the possibility of being passed a parameter called qCovarCol, which is currently just set to NULL.

I therefore have three questions:

  1. Is the --qCovarColList flag now obsolete or is it a feature that hasn't been implemented yet?
  2. If I added this flag to the step1_fitNULLGLMM.R script and then corrected the fitNULLGLMM() function so that it was passed to it correctly, will SAIGE then handle these columns appropriately?
  3. Since the --qCovarColList doesn't work, do we still have to pass all covariates to the --covarColList flag and ensure that categorical ones are encoded as (nCats-1) dummy variables?
samuelejones commented 2 years ago

Ok, I have just realised that the version of SAIGE at the new saigegit repo corresponds to the documentation I linked above. Will this version of SAIGE not be maintained anymore?

tydcg commented 9 months ago

Ok, I have just realised that the version of SAIGE at the new saigegit repo corresponds to the documentation I linked above. Will this version of SAIGE not be maintained anymore?

Have you solved it? I can't also find "--qCovarColList"... Is it the reason for the software version, please?