return.DE: Perform Differential Expression and Filter Results

In CellDEEP: Cell DiffErential Expression by Pooling ('CellDEEP')

Perform Differential Expression and Filter Results

Description

A wrapper for Seurat::FindMarkers that simplifies the extraction of Differentially Expressed (DE) genes. It supports p-value filtering and can return either gene names or a full results table.

Usage

return.DE(
  dataset,
  test.use = "wilcox",
  DE.ident.1,
  DE.ident.2,
  DE.group,
  assay = "RNA",
  p_cutoff = 0.05,
  name.only = TRUE,
  logfc.threshold = 0.25,
  min.pct = 0.01,
  full_list = FALSE,
  ...
)

Arguments

dataset	A Seurat object.
test.use	Character. DE test to use (default "wilcox").
DE.ident.1	Identifier(s) for the first group of cells.
DE.ident.2	Identifier(s) for the second group of cells.
DE.group	Character. Metadata column to group by.
assay	Character. Assay to use (default "RNA").
p_cutoff	Numeric. Adjusted p-value threshold (default 0.05).
name.only	Logical. If TRUE, return gene names only.
logfc.threshold	Numeric. Minimum log fold change (default 0.1).
min.pct	Numeric. Minimum fraction of cells expressing a gene.
full_list	Logical. If TRUE, return all genes and skip p-value filter.
...	Extra arguments passed to Seurat::FindMarkers.

Value

A character vector of genes or a marker data.frame.

CellDEEP documentation built on March 29, 2026, 5:08 p.m.