added min_cells_per_group to collapse counts function

}

#' @export

collapse_counts <- function(counts_mat, meta_data, varnames) {

collapse_counts <- function(counts_mat, meta_data, varnames, min_cells_per_group=0) {

    ## give each unique row a hash value for indexing

    hash <- compute_hash(meta_data, varnames)

    idx_keep <- which(!is.na(hash))

    design_collapsed <- data.frame(meta_data)[, varnames, drop = FALSE] %>% 

        cbind(sample_id = hash) %>% 

        unique()

    design_collapsed <- data.table(meta_data)[

        , varnames, drop = FALSE, with = FALSE

    ][

        , sample_id := hash

    ][

        , N := .N, by = sample_id

    ][

        N >= min_cells_per_group

    ] %>% 

    unique() %>% 

    dplyr::select(-N) %>% 

    data.frame()

    row.names(design_collapsed) <- design_collapsed$sample_id

    ## sum over samples