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weizhouUMICH / SAIGE

GNU Lesser General Public License v3.0
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"isSparse" not found #389

Closed oalavijeh closed 2 years ago

oalavijeh commented 2 years ago

Dear Wei,

Thank you such an amazing tool! I was trying to run SAIGE on a quantitative trait and when running SPA_test step2 I keep getting an error:

"Error in scoreTest_SAIGE_quantitativeTrait_sparseSigma(G0, obj.model.sub$obj.noK, : objest "isSparse' not found Execution halted

I have tried setting "isSparse" to TRUE,FALSE and just deleting it but this does not work.

I am working in an airlock using biobank data so cannot easily share code I am afraid but can offer screenshots if needed.

Many thanks for your help

weizhouUMICH commented 2 years ago

Hi @oalavijeh,

Which version of SAIGE are you using?

Thanks, Wei

oalavijeh commented 2 years ago

Dear Wei,

We are using SAIGE-GENE v0.42.1

Many thanks

Omid

weizhouUMICH commented 2 years ago

Hi Omid,

Sorry for my late reply.

We have just released a new version 1.0.0. It has computational efficiency improvements for both Step 1 and Step 2 for single-variant and set-based tests. We have created a new program github page https://github.com/saigegit/SAIGE with the documentation provided https://saigegit.github.io/SAIGE-doc/

The program will be maintained by multiple SAIGE developers there. Please feel free to try the version 1.0.0 and report issues if any.

Thanks! Wei