allow sum and mean collapsing (7f63f960) · Commits · github_fork / Presto 20250701

R/pseudobulk.R

+13 −7

Original line number	Diff line number	Diff line
		@@ -12,7 +12,7 @@ compute_hash <- function(data_df, vars_use) {
		}

		#' @export
		collapse_counts <- function(counts_mat, meta_data, varnames, min_cells_per_group=0, keep_n=FALSE) {
		collapse_counts <- function(counts_mat, meta_data, varnames, min_cells_per_group=0, keep_n=FALSE, how=c('sum', 'mean')[1]) {
		## give each unique row a hash value for indexing
		hash <- compute_hash(meta_data, varnames)
		idx_keep <- which(!is.na(hash))
		@@ -36,11 +36,6 @@ collapse_counts <- function(counts_mat, meta_data, varnames, min_cells_per_group
		] %>%
		unique() %>%
		data.frame()
		if (!keep_n) ({
		design_collapsed <- dplyr::select(design_collapsed, -N)
		})

		row.names(design_collapsed) <- design_collapsed$sample_id

		## sum over samples
		counts_collapsed <- presto:::sumGroups(counts_mat, hash, 1) %>% t()
		@@ -50,6 +45,17 @@ collapse_counts <- function(counts_mat, meta_data, varnames, min_cells_per_group
		## reorder to match design matrix
		counts_collapsed <- counts_collapsed[, design_collapsed$sample_id]
		design_collapsed$sample_id <- NULL


		if (how == 'mean') {
		counts_collapsed <- as.matrix(counts_collapsed %*% Matrix::Diagonal(x = 1 / design_collapsed$N))
		}
		if (!keep_n) {
		design_collapsed <- dplyr::select(design_collapsed, -N)
		}

		row.names(design_collapsed) <- design_collapsed$sample_id

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