-mat	Matrix, or file path of data.
-batchMat	Matrix or file path of batch table, which has at least three columns, including Samples matched colname of mat, Batch, and Covariates.
-cov	Specify the covariates besides batch, such as treatment condition, which can be used to model the outcome.
-log2trans	Boolean, specifying whether to do log2 transition before batch removal.
-pca	Boolean, specifying whether to do principle component analysis before and after batch removal.
-cluster	Boolean, specifing whether to do cluster analysis before and after batch removal.
-prefix	Character, specifying prefix of output figures, only needed if cluster/pca is TRUE.
-outdir	Output directory on disk.