This pull request is supposed to add rudimentary support for covariate adjustment during the batch-adjustment via sva::ComBat. Basically, columns of the $chipsamples data.frame in the ht12object can be specified in the parameter file (comma seperated string: c("covariate.1", "covariate.2", "covariate.3")) that will be added in the model matrix that is required by the ComBat()-function call, thus allowing for automatic adjustment during ComBat.
This is demonstrated in the vignette by simulating some random variables, specifying them in the parameter file and adjusting for them in the respective analysis step.
This pull request is supposed to add rudimentary support for covariate adjustment during the batch-adjustment via sva::ComBat. Basically, columns of the $chipsamples data.frame in the ht12object can be specified in the parameter file (comma seperated string:
c("covariate.1", "covariate.2", "covariate.3")) that will be added in the model matrix that is required by theComBat()-function call, thus allowing for automatic adjustment during ComBat.This is demonstrated in the vignette by simulating some random variables, specifying them in the parameter file and adjusting for them in the respective analysis step.