scCustomize (version 3.1.3)

exAM_Scoring: 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
)

Value

Seurat object

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).

References

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

Examples

if (FALSE) {
# Seurat
seurat_object <- exAM_Scoring(seurat_object = seurat_object, species = "human")
}