exAM_Scoring: Add exAM Gene List Module Scores

In scCustomize: Custom Visualizations & Functions for Streamlined Analyses of Single Cell Sequencing

Add exAM Gene List Module Scores

Description

Adds module scores from exAM genes from mouse and human.

Usage

exAM_Scoring(
  seurat_object,
  species,
  exam_module_name = NULL,
  method = "Seurat",
  ensembl_ids = FALSE,
  assay = NULL,
  overwrite = FALSE,
  exclude_unfound = FALSE,
  seed = 1
)

Arguments

seurat_object	object name.
species	Species of origin for given Seurat Object. Only accepted species are: mouse, human (name or abbreviation).
exam_module_name	name to use for the new meta.data column containing module scores.
method	method to use for module scoring, currently only "Seurat" is supported but more to be added. .
ensembl_ids	logical, whether feature names in the object are gene names or ensembl IDs (default is FALSE; set TRUE if feature names are ensembl IDs).
assay	Assay to use (default is the current object default assay).
overwrite	Logical. Whether to overwrite existing meta.data columns. Default is FALSE meaning that function will abort if columns with the name provided to exam_module_name is present in meta.data slot.
exclude_unfound	logical, whether to exclude features not present in current object (default is FALSE).
seed	seed for reproducibility (default is 1).

Value

Seurat object

References

Gene list is from: SI Table 22 Marsh et al., 2022 (Nature Neuroscience) from \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1038/s41593-022-01022-8")}. See data-raw directory for scripts used to create gene list.

Examples

## Not run: 
# Seurat
seurat_object <- exAM_Scoring(seurat_object = seurat_object, species = "human")

## End(Not run)

scCustomize documentation built on Aug. 26, 2025, 9:08 a.m.