I tried using the BGEN file format in the second step, but it keeps throwing an error like below. I've looked into a bunch of stuff but can't figure it out. I am wondering if it's a bug in the script. It looks like a function called "scoreTest_SPAGMMAT_survivalTrait_cond_sparseSigma" was not defined in the main script.
...
numPassMarker: 20
user system elapsed
2.868 2.650 2.549
[1] 64
numPassMarker: 21
user system elapsed
2.897 2.699 2.555
[1] 66
numPassMarker: 22
user system elapsed
2.928 2.744 2.559
[1] 68
numPassMarker: 23
Error in scoreTest_SPAGMMAT_survivalTrait_cond_sparseSigma(g, g_mc, AC2, :
could not find function "scoreTest_SPAGMMAT_survivalTrait_cond_sparseSigma"
Calls: SPAGMMATtest -> scoreTest_SAIGE_survivalTrait_cond_sparseSigma
Execution halted
I tried using the BGEN file format in the second step, but it keeps throwing an error like below. I've looked into a bunch of stuff but can't figure it out. I am wondering if it's a bug in the script. It looks like a function called "scoreTest_SPAGMMAT_survivalTrait_cond_sparseSigma" was not defined in the main script. ... numPassMarker: 20 user system elapsed 2.868 2.650 2.549 [1] 64 numPassMarker: 21 user system elapsed 2.897 2.699 2.555 [1] 66 numPassMarker: 22 user system elapsed 2.928 2.744 2.559 [1] 68 numPassMarker: 23 Error in scoreTest_SPAGMMAT_survivalTrait_cond_sparseSigma(g, g_mc, AC2, : could not find function "scoreTest_SPAGMMAT_survivalTrait_cond_sparseSigma" Calls: SPAGMMATtest -> scoreTest_SAIGE_survivalTrait_cond_sparseSigma Execution halted