I would like to use SAIGE with GWAS. The data are in plink format and contain missing values.
I performed step 1 with no issues. For step 2, I understand I cannot use plink files.
Error with:
379743 samples have been used to fit the glmm null model
[1] "Leave-one-chromosome-out is not applied"
Single variance ratio is provided, so categorical variance ratio won't be used!
variance Ratio is 1.001402
487409 sample IDs are found in sample file
isCondition is FALSE
Error in SPAGMMATtest(bgenFile = paste0("./Imputation/", "ukb_imp_chr", :
ERROR!471 samples used in glmm model fit do not have dosages
Execution halted
I have read some tips, should i updata my SAIGE(version 0.44.6.4)
Besides, in step1, I have set LOCO = TRUE, but result showed the "Leave-one-chromosome-out is not applied".
I would like to use SAIGE with GWAS. The data are in plink format and contain missing values. I performed step 1 with no issues. For step 2, I understand I cannot use plink files.
Error with:
379743 samples have been used to fit the glmm null model [1] "Leave-one-chromosome-out is not applied" Single variance ratio is provided, so categorical variance ratio won't be used! variance Ratio is 1.001402 487409 sample IDs are found in sample file isCondition is FALSE Error in SPAGMMATtest(bgenFile = paste0("./Imputation/", "ukb_imp_chr", : ERROR!471 samples used in glmm model fit do not have dosages Execution halted
I have read some tips, should i updata my SAIGE(version 0.44.6.4)
Besides, in step1, I have set LOCO = TRUE, but result showed the "Leave-one-chromosome-out is not applied".
The problem have confused me seriously.
Appreciate for any solution methods.