extract_sc_data: Extract data frame

In IOBR/IOBR: Immune Oncology Biological Research

Extract data frame

Description

Extract and combine data frame with cells as rows and features as columns from Seurat assay data.

Usage

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

Arguments

sce	Seurat object
vars	Vector of variables as features
assay	Assay to pull data from
slot	Specific assay data to get or set
combine_meta_data	Whether to combine metadata with the extracted data frame

Value

Data frame with cells as rows and features as columns

Author(s)

Dongqiang Zeng

Examples

#Load data
data("pbmc_small")
pbmc_small
#Choose features
vars<-c("PPBP", "IGLL5", "VDAC3", "CD1C", "AKR1C3", "PF4", "MYL9", "GNLY", "TREML1", "CA2")
#Get extracted data frame
eset<-extract_sc_data(sce= pbmc_small, vars= vars, assay= "RNA")

IOBR/IOBR documentation built on May 5, 2024, 2:34 p.m.