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zhanxw / rvtests

Rare variant test software for next generation sequencing data
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How to hide the covariate results from the output from SKAT and Burden test #103

Open suraj86nong opened 4 years ago

suraj86nong commented 4 years ago

Hi, I am getting the full range of covariate results in the output from the SKAT and Burden test. Is there any option to hide the covariate effect from the output. I tried hide-covar, but it does not work.

julie-lake commented 2 years ago

I'm having the same issue, when I run the cmcWald burden test I can't hide the covariate effects even when using --hide-covar.

Does the first (non-header) line in this example correspond to the gene effect adjusted for covariates?

Gene RANGE N_INFORMATIVE NumVar NumPolyVar NonRefSite Beta SE Pvalue SAMD11 1:923922-944574,1:923922-944574,1:925730-944574 7974 26 26 241 0.134509 0.144036 0.350379 SAMD11 1:923922-944574,1:923922-944574,1:925730-944574 7974 26 26 241 -0.608945 0.0497047 1.65393e-34 SAMD11 1:923922-944574,1:923922-944574,1:925730-944574 7974 26 26 241 -0.0493553 0.00180854 5.54079e-164 SAMD11 1:923922-944574,1:923922-944574,1:925730-944574 7974 26 26 241 -2.97423 0.420803 1.57192e-12 SAMD11 1:923922-944574,1:923922-944574,1:925730-944574 7974 26 26 241 1.21688 0.800385 0.128419 SAMD11 1:923922-944574,1:923922-944574,1:925730-944574 7974 26 26 241 13.8824 0.935202 7.58002e-50 SAMD11 1:923922-944574,1:923922-944574,1:925730-944574 7974 26 26 241 0.499414 0.940748 0.59551 SAMD11 1:923922-944574,1:923922-944574,1:925730-944574 7974 26 26 241 0.656717 1.05306 0.532872