I am very new to R-SAIGE. I tried to follow https://github.com/weizhouUMICH/SAIGE/issues/272 to install SAIGE package and run your example. I typed "step1_fitNULLGLMM.R --help
step2_SPAtests.R --help
createSparseGRM.R --help"
They all worked. However, I always got the following output when I ran your example. Could you please let me know you suggestions to help solve the problem? Many thanks!
tauInit is 0 0
cateVarRatioMinMACVecExclude is 0.5 1.5 2.5 3.5 4.5 5.5 10.5 20.5
cateVarRatioMaxMACVecInclude is 1.5 2.5 3.5 4.5 5.5 10.5 20.5
Markers in the Plink file with MAF >= 0.01 will be used to construct GRM
Error in fitNULLGLMM(plinkFile = opt$plinkFile, phenoFile = opt$phenoFile, :
WARNING: The variance ratio file ~/.varianceRatio.txt already exists. The new variance ratios will be output to ~/.varianceRatio.txt. In order to avoid overwriting the file, please remove the ~/.varianceRatio.txt or use the argument outputPrefix_varRatio to specify a different prefix to output the variance ratio(s). Otherwise, specify IsOverwriteVarianceRatioFile=TRUE so the file will be overwritten with new variance ratio(s)
Execution halted
zsh: command not found: --plinkFile=nfam_100_nindep_0_step1_includeMoreRareVariants_poly
zsh: command not found: --phenoFile=pheno_1000samples.txt_withdosages_withBothTraitTypes.txt
Hello,
I am very new to R-SAIGE. I tried to follow https://github.com/weizhouUMICH/SAIGE/issues/272 to install SAIGE package and run your example. I typed "step1_fitNULLGLMM.R --help step2_SPAtests.R --help createSparseGRM.R --help" They all worked. However, I always got the following output when I ran your example. Could you please let me know you suggestions to help solve the problem? Many thanks!
step1_fitNULLGLMM.R \
Loading required package: optparse R version 4.0.5 (2021-03-31) Platform: x86_64-apple-darwin13.4.0 (64-bit) Running under: macOS Big Sur 10.16
Matrix products: default BLAS/LAPACK: /Users/briolaisnew2/opt/anaconda3/envs/saige/lib/libopenblasp-r0.3.17.dylib
locale: [1] en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8
attached base packages: [1] stats graphics grDevices utils datasets methods base
other attached packages: [1] optparse_1.6.6 SAIGE_0.44.5
loaded via a namespace (and not attached): [1] compiler_4.0.5 Matrix_1.3-4 Rcpp_1.0.7 getopt_1.20.3
[5] grid_4.0.5 RcppParallel_5.1.4 lattice_0.20-44
$plinkFile [1] ""
$phenoFile [1] ""
$phenoCol [1] ""
$traitType [1] "binary"
$invNormalize [1] FALSE
$covarColList [1] ""
$sampleIDColinphenoFile [1] "IID"
$tol [1] 0.02
$maxiter [1] 20
$tolPCG [1] 1e-05
$maxiterPCG [1] 500
$nThreads [1] 1
$SPAcutoff [1] 2
$numRandomMarkerforVarianceRatio [1] 30
$skipModelFitting [1] FALSE
$memoryChunk [1] 2
$tauInit [1] "0,0"
$LOCO [1] TRUE
$traceCVcutoff [1] 0.0025
$ratioCVcutoff [1] 0.001
$outputPrefix [1] "~/"
$IsOverwriteVarianceRatioFile [1] FALSE
$IsSparseKin [1] FALSE
$numRandomMarkerforSparseKin [1] 2000
$isCateVarianceRatio [1] FALSE
$relatednessCutoff [1] 0.125
$cateVarRatioMinMACVecExclude [1] "0.5,1.5,2.5,3.5,4.5,5.5,10.5,20.5"
$cateVarRatioMaxMACVecInclude [1] "1.5,2.5,3.5,4.5,5.5,10.5,20.5"
$isCovariateTransform [1] TRUE
$isDiagofKinSetAsOne [1] FALSE
$useSparseSigmaConditionerforPCG [1] FALSE
$useSparseSigmaforInitTau [1] FALSE
$useSparseGRMtoFitNULL [1] FALSE
$minMAFforGRM [1] 0.01
$minCovariateCount [1] -1
$includeNonautoMarkersforVarRatio [1] FALSE
$FemaleOnly [1] FALSE
$MaleOnly [1] FALSE
$sexCol [1] ""
$FemaleCode [1] "1"
$MaleCode [1] "0"
$noEstFixedEff [1] FALSE
$help [1] FALSE
tauInit is 0 0 cateVarRatioMinMACVecExclude is 0.5 1.5 2.5 3.5 4.5 5.5 10.5 20.5 cateVarRatioMaxMACVecInclude is 1.5 2.5 3.5 4.5 5.5 10.5 20.5 Markers in the Plink file with MAF >= 0.01 will be used to construct GRM Error in fitNULLGLMM(plinkFile = opt$plinkFile, phenoFile = opt$phenoFile, : WARNING: The variance ratio file ~/.varianceRatio.txt already exists. The new variance ratios will be output to ~/.varianceRatio.txt. In order to avoid overwriting the file, please remove the ~/.varianceRatio.txt or use the argument outputPrefix_varRatio to specify a different prefix to output the variance ratio(s). Otherwise, specify IsOverwriteVarianceRatioFile=TRUE so the file will be overwritten with new variance ratio(s) Execution halted zsh: command not found: --plinkFile=nfam_100_nindep_0_step1_includeMoreRareVariants_poly zsh: command not found: --phenoFile=pheno_1000samples.txt_withdosages_withBothTraitTypes.txt