Get NAs for Est, SE, Wald.stat and Wald.pval

smgogarten / GWASTools

Classes for storing very large GWAS data sets and annotation, and functions for GWAS data cleaning and analysis

https://bioconductor.org/packages/GWASTools

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Get NAs for Est, SE, Wald.stat and Wald.pval #9

Closed ryshi06 closed 11 months ago

ryshi06 commented 3 years ago

Hi there,

I am sorry to bother again. I have tried the assocCoxPH function with a well-built genoData, but after a long-time wait, I found the columns after Est are all NAs. Are there any possible reasons explaining this? I have got no errors or warnings during the running process.

Best, Ruyu

smgogarten commented 3 years ago

That means the coxph function is unable to return a value for the test. It's run inside a tryCatch block in case the test fails for some variants but not for others, but in your case it seems to be failing for all variants. I'd suggest extracting genotypes for a few variants and trying to run the test directly. coxph might give you some more informative error messages about what's going wrong.