Update pseudobulk.R (0aa8def4) · Commits · github_fork / Presto 20250701

R/pseudobulk.R

+10 −2

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, collapse_background=TRUE) {
		min_counts_per_sample=10, present_in_min_samples=5, collapse_background=TRUE, vals_test=NULL) {
		message('WARNING: meta_data should only contain pseudobulk identifying variables')

		## filter low expressed genes
		@@ -58,7 +58,15 @@ pseudobulk_deseq2 <- function(dge_formula, meta_data, counts_df, verbose=TRUE,
		if (verbose) {
		message(sprintf('Contrast var: %s', contrast_var))
		}
		Reduce(rbind, lapply(unique(meta_data[[contrast_var]]), function(foreground_id) {
		if (is.null(vals_test)) {
		vals_test <- unique(meta_data[[contrast_var]])
		} else {
		if (any(!vals_test %in% unique(meta_data[[contrast_var]]))) {
		stop('vals_test must be values in the contrast var')
		}
		}

		Reduce(rbind, lapply(vals_test, function(foreground_id) {
		if (verbose) {
		message(foreground_id)
		}