Update pseudobulk.R (d7c0ddf1) · Commits · github_fork / Presto 20250701

R/pseudobulk.R

+6 −4

Original line number	Diff line number	Diff line
		@@ -39,7 +39,7 @@ collapse_counts <- function(counts_mat, meta_data, varnames) {
		}
		#' @export
		pseudobulk_deseq2 <- function(dge_formula, meta_data, counts_df, verbose=TRUE,
		min_counts_per_sample=10, present_in_min_samples=5) {
		min_counts_per_sample=10, present_in_min_samples=5, collapse_background=TRUE) {
		message('WARNING: meta_data should only contain pseudobulk identifying variables')

		## filter low expressed genes
		@@ -70,10 +70,12 @@ pseudobulk_deseq2 <- function(dge_formula, meta_data, counts_df, verbose=TRUE,
		'background'))

		## background clusters should not be treated as independent observations
		# res <- collapse_counts(counts_df, design, all_vars)
		if (collapse_background) {
		res <- collapse_counts(counts_df, design, colnames(design))
		design <- res$meta_data
		counts_df <- res$counts_mat
		}
		# res <- collapse_counts(counts_df, design, all_vars)

		## Do DGE with DESeq2
		dds <- DESeqDataSetFromMatrix(