extract_sc_data: Extract Data Frame from Seurat Object

In IOBR: Immune Oncology Biological Research

Extract Data Frame from Seurat Object

Description

Extracts and combines a data frame with cells as rows and features as columns from Seurat assay data. Supports multiple assays and optional metadata integration.

Usage

extract_sc_data(
  sce,
  vars = NULL,
  assay,
  slot = "scale.data",
  combine_meta_data = TRUE
)

Arguments

sce	Seurat object.
vars	Character vector of feature names to extract. If 'NULL', all features are extracted.
assay	Character vector specifying assay(s) to pull data from.
slot	Character string specifying the assay data slot. Default is '"scale.data"'.
combine_meta_data	Logical indicating whether to combine metadata with the extracted data frame. Default is 'TRUE'.

Value

Data frame with cells as rows and features as columns.

Author(s)

Dongqiang Zeng

Examples

if (requireNamespace("Seurat", quietly = TRUE)) {
  pbmc <- SeuratObject::pbmc_small
  vars <- c("PPBP", "IGLL5", "VDAC3", "CD1C", "AKR1C3")
  eset <- extract_sc_data(sce = pbmc, vars = vars, assay = "RNA")
}

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