Perform Differential Expression and Filter Results

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.

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.