Add exAM Gene List Module Scores — exAM

Adds module scores from exAM genes from mouse and human.

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 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")
}