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saigegit / SAIGE

Development for SAIGE and SAIGE-GENE(+)
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Conditional analysis - step 2 #21

Closed damichalek closed 2 years ago

damichalek commented 2 years ago

Hi,

I have used SAIGE (v1.0.1) for conditional analysis. When I try --condition with only one SNP, then conditional analysis works, but when I add second SNP I got an error (I separate SNPs with coma).

Error in assign_conditionMarkers_factors(genoType, condition_genoIndex_prev_a,  : 
  inv(): matrix is singular
Calls: SPAGMMATtest -> assign_conditionMarkers_factors
Execution halted

If you need more information, please let me know. Thank you!

saigegit commented 2 years ago

Hi @damichalek,

This error is because the conditional markers are not specified in the order of chromosome and position. For example, it should be --condition=1:4:A:C,1:9:A:C instead of --condition=1:9:A:C,1:4:A:C.

Thanks, Wei

damichalek commented 2 years ago

Hi Wei,

I forgot to mention that the issue was resolved, since we have talked about it few days ago. Thank you for your help!