in correct_counts, specify exact levels to remove

#' @export 

correct_counts <- function(object, effects_remove, umi_common, verbose=0) {

correct_counts <- function (object, effects_remove, umi_common, verbose = 0) 

{

    if (missing(umi_common)) {

        umi_common <- mean(log(Matrix::colSums(object$response)))

#         umi_common <- exp(mean(object$meta_data$EXPOSURE))

    }

    ## read depth should not be removed but equalized

    effects_remove <- setdiff(effects_remove, 'EXPOSURE')

    effects_remove <- setdiff(effects_remove, "EXPOSURE")

    idx_keep <- object$betanames_df %>% 

        tibble::rowid_to_column('idx') %>% 

        subset(!grepl(paste(effects_remove, collapse = '|'), grpvar)) %>% 

        tibble::rowid_to_column("idx") %>% 

#         subset(!grepl(paste(effects_remove, collapse = "|"), grpvar)) %>% 

        subset(!grpvar %in% effects_remove) %>% 

        with(idx)

    if (verbose > 0) {

        message('remove')

        object$betanames_df[-idx_keep, ] %>% with(unique(grpvar)) %>% print()

        message('preserve')

        object$betanames_df[idx_keep, ] %>% with(unique(grpvar)) %>% print()        

        message("remove")

        object$betanames_df[-idx_keep, ] %>% with(unique(grpvar)) %>% 

            print()

        message("preserve")

        object$betanames_df[idx_keep, ] %>% with(unique(grpvar)) %>% 

            print()

    }

#     b1 <- object$beta[which(object$betanames_df$grpvar == 'EXPOSURE'), ]

    design_keep <- object$design[idx_keep, ]

    design_keep['EXPOSURE', ] <- umi_common

    effect_keep <- exp(Matrix::crossprod(design_keep, object$beta[idx_keep, ]))

    design_keep["EXPOSURE", ] <- umi_common

    effect_keep <- exp(Matrix::crossprod(design_keep, object$beta[idx_keep, 

        ]))

    object$corrected <- Matrix::t(effect_keep + object$epsilon)

    object$corrected <- as(object$corrected, class(object$response)[[1]])

    colnames(object$corrected) <- colnames(object$response)

    row.names(object$corrected) <- row.names(object$response)

    return(object)

}