Extract Data Frame from Seurat Object — extract_sc

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

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")
}
#> ℹ Available assays: "RNA"
#> ℹ Merging metadata...