fixed background collapsing

    ## reorder to match design matrix

    counts_collapsed <- counts_collapsed[, design_collapsed$sample_id]

    design_collapsed$sample_id <- NULL

    return(list(counts_mat = counts_collapsed, meta_data = design_collapsed))

}

#' @export

pseudobulk_deseq2 <- function(dge_formula, meta_data, counts_df, verbose=TRUE, 

                   min_counts_per_sample=10, present_in_min_samples=5) {

    message('WARNING: meta_data should only contain pseudobulk identifying variables')

    ## filter low expressed genes

    genes_keep <- which(Matrix::rowSums(counts_df >= min_counts_per_sample) >= present_in_min_samples)

    if (verbose) {

            ## setup design 

            design <- meta_data            

            design[[contrast_var]] <- factor(ifelse(design[[contrast_var]] == foreground_id,

                                               paste0('cluster', foreground_id), 

                                               paste0('cluster_', foreground_id), 

                                               'background'))

            ## background clusters should not be treated as independent observations

            res <- collapse_counts(counts_df, design, all_vars)

#             res <- collapse_counts(counts_df, design, all_vars)

            res <- collapse_counts(counts_df, design, colnames(design))

            design <- res$meta_data

            counts_df <- res$counts_mat

            print(head(design))

            ## Do DGE with DESeq2

            dds <- DESeqDataSetFromMatrix(

                countData = counts_df,

        return(dge_res)

    })) %>% 

    dplyr::select(group, feature, dplyr::everything())

}

#' @export