FindMarker.CellDEEP: Differential Expression with Optional Cell Pooling

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

Differential Expression with Optional Cell Pooling

Description

It can run Seurat DE directly or first aggregate cells into metacells using CellDEEP pooling.

Usage

FindMarker.CellDEEP(
  object,
  ident.1 = NULL,
  ident.2 = NULL,
  group.by = "group_id",
  sample_id = NULL,
  group_id = NULL,
  cluster_id = NULL,
  prepare = TRUE,
  test.use = "wilcox",
  Pool = TRUE,
  readcounts = "sum",
  n_cells = 10,
  assay = "RNA",
  min_cells_per_subgroup = 25,
  cell_selection = "kmean",
  name.only = TRUE,
  logfc.threshold = 0.25,
  min.pct = 0.01,
  p_cutoff = 0.05,
  full_list = FALSE,
  ...
)

Arguments

object	A Seurat object.
ident.1	Character. First identity group to compare.
ident.2	Character. Second identity group to compare.
group.by	Character. Metadata column used for grouping (default "group_id").
sample_id	Character. Input metadata column for sample IDs.
group_id	Character. Input metadata column for group IDs.
cluster_id	Character. Input metadata column for cluster IDs.
prepare	Logical. If TRUE, run prepare_data first.
test.use	Character. DE test to use.
Pool	Logical. If TRUE, perform CellDEEP pooling before DE (default TRUE).
readcounts	Character. Pool aggregation method: "sum", "mean", or "10X".
n_cells	Integer. Target number of cells per pool.
assay	Character. Assay to use (default "RNA").
min_cells_per_subgroup	Integer. Minimum cells in each sample-cluster subgroup required for pooling.
cell_selection	Character. Pooling strategy: "kmean" or "random".
name.only	Logical. If TRUE, return gene names only.
logfc.threshold	Numeric. Minimum log fold-change.
min.pct	Numeric. Minimum detection rate.
p_cutoff	Numeric. Adjusted p-value threshold.
full_list	Logical. If TRUE, return all genes regardless of p-value.
...	Additional arguments passed to Seurat::FindMarkers.

Value

A vector of gene names or a DE data.frame.

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