Can SAIGE handle NAs in phenotype file

weizhouUMICH / SAIGE

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Can SAIGE handle NAs in phenotype file #372

Closed adanordeidet closed 2 years ago

adanordeidet commented 2 years ago

Hi,

I want to perform single-variant association tests, and I have one file containing data on multiple binary phenotypes (one column for each phenotype, with 1/0/NA). I know that I have to run step1 for each phenotype (specified by phenoCol) and that it has to be 1 and 0 in the phenotype column. But I want to know if there can be NAs as well?

If there cannot be NAs, I guess I will have to make one phenotype file for each phenotype, to only have 1 and 0 in the column.

weizhouUMICH commented 2 years ago

Hi @adanordeidet,

Yes, any sample with missing (NA) for the phenotype or any covariates will be removed from the analysis.

Thanks, Wei