Open marlenebrs opened 2 years ago
I performed a CMC Wald burden test on my phenotype "EP" adjusted on 6 covariates : sex, AGE, PC1, PC2, PC3 and BMI. My output shows for each gene 7 duplicated lines. What does each line mean? Does a line correspond to a fit on all covariates?
Here is a part of my output :
Gene RANGE N_INFORMATIVE NumVar NumPolyVar NonRefSite Beta SE Pvalue FAM87B 1:817370-819834 69 41 41 41 -0.502387 0.568318 0.376702 FAM87B 1:817370-819834 69 41 41 41 1.61057 0.69236 0.0200079 FAM87B 1:817370-819834 69 41 41 41 -0.00472976 0.0244506 0.846614 FAM87B 1:817370-819834 69 41 41 41 118.706 187.67 0.527045 FAM87B 1:817370-819834 69 41 41 41 -189.578 446.778 0.671331 FAM87B 1:817370-819834 69 41 41 41 -96.8701 127.91 0.448851 FAM87B 1:817370-819834 69 41 41 41 -0.023334 0.0482548 0.628699 LINC00115 1:826205-827522 69 29 29 29 -0.44987 0.587963 0.444192 LINC00115 1:826205-827522 69 29 29 29 1.58764 0.690461 0.0214826 LINC00115 1:826205-827522 69 29 29 29 -0.00530215 0.0245051 0.8287 LINC00115 1:826205-827522 69 29 29 29 104.702 183.388 0.568046 LINC00115 1:826205-827522 69 29 29 29 -155.349 439.247 0.723585 LINC00115 1:826205-827522 69 29 29 29 -93.4759 126.892 0.461333 LINC00115 1:826205-827522 69 29 29 29 -0.0230046 0.0480832 0.632341
Here is my command line :
rvtest --inVcf input.vcf.gz --pheno pheno.ped --pheno-name EP --covar covars.ped --covar-name sex,AGE,PC1,PC2,PC3,BMI --out output --geneFile refFlat_hg38.txt.gz --burden cmcWald
I performed a CMC Wald burden test on my phenotype "EP" adjusted on 6 covariates : sex, AGE, PC1, PC2, PC3 and BMI. My output shows for each gene 7 duplicated lines. What does each line mean? Does a line correspond to a fit on all covariates?
Here is a part of my output :
Here is my command line :
rvtest --inVcf input.vcf.gz --pheno pheno.ped --pheno-name EP --covar covars.ped --covar-name sex,AGE,PC1,PC2,PC3,BMI --out output --geneFile refFlat_hg38.txt.gz --burden cmcWald