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weizhouUMICH / SAIGE

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SAIGE-0.44.6.1 step2_SPAtests.R Error #371

Closed liwangchang closed 2 years ago

liwangchang commented 2 years ago

1000 samples were used in fitting the NULL glmm model and are found in sample file sparse kinship matrix is not used Missing dosages will be mean imputed for the analysis Analysis started at 1632365348 Seconds minMAC: 1 minMAF: 1e-04 Minimum MAF of markers to be tested is 5e-04 It is a binary trait Analyzing 0 cases and 0 controls isCondition is FALSE Analysis started at 1632365348 Seconds Error in obj.null$XV %*% G : requires numeric/complex matrix/vector arguments Calls: SPAGMMATtest ... scoreTest_SAIGE_binaryTrait_cond_sparseSigma -> Score_Test Execution halted

What causes this error

weizhouUMICH commented 2 years ago

Sorry for the 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. The docker image has been updated. Please feel free to try the version 1.0.0 and report issues if any.

Thanks! Wei