jtleek/sva-devel — pull request #2 by wevanjohnson (2014-12-17 21:21:06+00:00)
Title: Made several modifications to ComBat to streamline the design matrix set...

...up and to prepare for future modifications (mean-only batch adjustment, multiple batches, confounded designs, etc). More specifically, I did the following: (1) added a default value for the 'mod' parameter (mod=NULL), (2) removed the numCovs argument; the user is required to supply the covariate matrix, so distinguishing between categorical and numerical covariates is no longer necessary, (3) removed the dependancy on helper functions such as filter.absent (this is not currently used anyway), build.design, design.mat, list.batch, and (4) removed the statment that 'multiple batches are allowed'. This version of ComBat does not robustly handle multiple batches.