generateRef_seurat: Generate Reference Matrix from Seurat Object

In IOBR: Immune Oncology Biological Research

Generate Reference Matrix from Seurat Object

Description

Generates reference gene expression data from a Seurat object by identifying marker genes for each cell type and aggregating expression data.

Usage

generateRef_seurat(
  sce,
  celltype = NULL,
  proportion = NULL,
  assay_deg = "RNA",
  slot_deg = "data",
  adjust_assay = FALSE,
  assay_out = "RNA",
  slot_out = "data",
  verbose = FALSE,
  only.pos = TRUE,
  n_ref_genes = 50,
  logfc.threshold = 0.15,
  test.use = "wilcox"
)

Arguments

sce	Seurat object containing single-cell RNA-seq data.
celltype	Character. Cell type column name in metadata. Default is 'NULL' (uses default identity).
proportion	Numeric. Proportion of cells to randomly select for analysis. Default is 'NULL' (use all cells).
assay_deg	Character. Assay for finding markers. Default is '"RNA"'.
slot_deg	Character. Slot for finding markers. Default is '"data"'.
adjust_assay	Logical. Whether to adjust assay for SCT. Default is 'FALSE'.
assay_out	Character. Assay for output. Default is '"RNA"'.
slot_out	Character. Slot for output. Default is '"data"'.
verbose	Logical. Print verbose messages. Default is 'FALSE'.
only.pos	Logical. Return only positive markers. Default is 'TRUE'.
n_ref_genes	Integer. Number of reference genes per cell type. Default is 50.
logfc.threshold	Numeric. Log fold change threshold. Default is 0.15.
test.use	Character. Statistical test for marker identification. Default is '"wilcox"'.

Value

Matrix containing aggregated expression data for reference genes.

Author(s)

Dongqiang Zeng

Examples

## Not run: 
if (requireNamespace("Seurat", quietly = TRUE)) {
  # Requires a Seurat object with sufficient cells and markers
  sm <- generateRef_seurat(sce = seurat_obj, celltype = "cell_type", slot_out = "data")
}

## End(Not run)

IOBR documentation built on May 30, 2026, 5:07 p.m.