Thank you for creating and maintaining this software.
In the wiki, you state that
Note: Missing data in the covariate file can be labeled by any non-numeric value (e.g. NA). They will be automatically imputed to the mean value in the data file.
However, samples with missing covariates are simply dropped from my analysis, per the .log file when running SKAT, CMC, FamCMC, FamSKAT:
[WARN] Total [ 63 ] samples are dropped from VCF file due to missing covariate.
How should I assure that my samples with missing covariates are not dropped?
For reference, here's a simplified version of my codewhen running FamSKAT + FamCMC:
rvtest --inVcf exons.vcf.gz --pheno phenos.txt --pheno-name dft --freqUpper 0.01 --impute drop --covar cov.txt --covar-name AgeAtExam,Sex,V7,V8,V9,WV,ChipNum,CohortNum,PC1_C12,PC2_C12,PC3_C12 --geneFile refFlat_hg19.txt.gz --burden famcmc --kernel famskat --kinship C1C2.kinship --numThread 3 --out output;
(Note, I tried removing the --impute drop flag, which prevents imputation of missing genotypes, but this doesn't alter covariate dropping)
Thank you in advance,
Katya
Thank you for creating and maintaining this software.
In the wiki, you state that
However, samples with missing covariates are simply dropped from my analysis, per the .log file when running SKAT, CMC, FamCMC, FamSKAT:
How should I assure that my samples with missing covariates are not dropped?
For reference, here's a simplified version of my codewhen running FamSKAT + FamCMC:
rvtest --inVcf exons.vcf.gz --pheno phenos.txt --pheno-name dft --freqUpper 0.01 --impute drop --covar cov.txt --covar-name AgeAtExam,Sex,V7,V8,V9,WV,ChipNum,CohortNum,PC1_C12,PC2_C12,PC3_C12 --geneFile refFlat_hg19.txt.gz --burden famcmc --kernel famskat --kinship C1C2.kinship --numThread 3 --out output;(Note, I tried removing the --impute drop flag, which prevents imputation of missing genotypes, but this doesn't alter covariate dropping)
Thank you in advance,
Katya