search

weizhou0 / GATE

GNU Lesser General Public License v3.0
19 stars 9 forks source link

adjust for categorical covariates #4

Closed lisongmiller closed 3 years ago

lisongmiller commented 3 years ago

Hi there,

Thanks for developing this nice tool! I would like run a GWAS for time to event outcome, and adjusting several covariates, including nominal covariates. And I notice there is a flag "--covarColList=COVARCOLLIST" in docker image, which is different from SAIGE. I am not sure whether GATE supports for adjusting nominal covariates?

If not, I learnt that for linear regression, you can regress all covarites then use residual for GWAS. Is there a similar way for survival analysis? Thank you! { For example, in R fit = lm(phenotype ~ covariates, data) corrected_phenotype = resid(fit) }

Best, Song

weizhou0 commented 3 years ago

Hi Song,

Thanks for using GATE! --covarColList is the same as SAIGE and currently GATE does not support the categorical covariates automatically. You will need to write the different categories to different columns in the covariate file. GATE does not support regressing out covariates first, but we will implement a similar option soon.

Thanks, Wei

On Fri, Feb 12, 2021 at 6:53 AM lisongmiller notifications@github.com wrote:

Hi there,

Thanks for developing this nice tool! I would like run a GWAS for time to event outcome, and adjusting several covariates, including nominal covariates. And I notice there is a flag "--covarColList=COVARCOLLIST" in docker image, which is different from SAIGE. I am not sure whether GATE supports for adjusting nominal covariates?

If not, I learnt that for linear regression, you can regress all covarites then use residual for GWAS. Is there a similar way for survival analysis? Thank you! { For example, in R fit = lm(phenotype ~ covariates, data) corrected_phenotype = resid(fit) }

Best, Song

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/weizhou0/GATE/issues/4, or unsubscribe https://github.com/notifications/unsubscribe-auth/APJSQMSY6PUAWVLSJTWKTJ3S6UJDFANCNFSM4XQRZINA .

lisongmiller commented 3 years ago

Hi Wei,

Thanks for you reply, very helpful! Mind if I ask the approximate date of new GATE repository release. If just a couple of weeks then I would rather wait for it.

Best, Song