Convert muscat::pbDS() results into a flat list of data frames compatible with DeeDeeExperiment

This helper function extracts and flattens the nested structure returned by muscat::pbDS(), returning one table per contrast–cluster combination. Each resulting data frame will have standardized column names (log2FoldChange, pvalue, padj).

Usage

muscat_list_for_dde(res, padj_col = c("p_adj.loc", "p_adj.glb"))

Arguments

res

A list, typically the output of muscat::pbDS() function, containing one or more contrasts

padj_col

A character string specifying which adjusted p-value column to extract. It can be either "p_adj.loc" or "p_adj.glb".

Value

A named list of data frames

Details

The function is intended to simplify the integration of muscat results into a DeeDeeExperiment object. It automatically renames columns (logFC to log2FoldChange, p_val to pvalue, and the selected adjusted p-value column to padj) and annotates the resulting list with metadata about the originating package.

The function checks that each contrast entry contains a valid table component as expected from pbDS() output. Invalid or empty contrasts are skipped with a warning message. The names of the list elements in res must match contrast names found in the table slot of each entry.

Examples

data("muscat_pbDS_res", package = "DeeDeeExperiment")
new_muscat_list <- muscat_list_for_dde(list(`stim-ctrl` = muscat_res))
#> ℹ Returning 3 muscat contrast-cluster tables formatted for DeeDeeExperiment