Prepare Immune Dictionary references

Prepare cell-type reference objects and signatures used by RunIREA().

Usage

PrepareIREA(
  species = c("Homo_sapiens", "Mus_musculus"),
  db = "IREA_NK_cell",
  db_update = FALSE,
  data_dir = NULL,
  verbose = TRUE,
  ...
)

Arguments

species: "Homo_sapiens" or "Mus_musculus".
db: Reference selectors such as "IREA_NK_cell" or "IREA_Macrophage". The suffix is the exact portal cell-type identifier.
db_update: Force a refresh. FALSE loads the cache when available.
data_dir: Directory or named list of local source files. Searches data_dir/<db>/ then data_dir. Named lists override a path, e.g. list(MSigDB = "~/db/msigdb").
verbose: Whether to print the message. Default is TRUE.
...: Passed to helper functions.

Value

A named species list with an irea_reference under each selector. Each reference contains object, cytokine, polarization, cell_type, species, paths, checksum_md5 and provenance. Expression rows are mouse genes; columns are reference cells in their original order.

Details

Missing files are downloaded from the official portal. Source assets are unversioned; the cache manifest records their checksums and rejects changed files unless db_update = TRUE. Named data_dir lists may use the selector or "IREA". Each file is searched under the selector subdirectory before the parent directory. Human input uses partial orthologue mappings; the expression reference remains mouse lymph-node cells. Files are not bundled.

References

Cui, Ang; Huang, Teddy; Li, Shuqiang; Ma, Aileen; Perez, Jorge L.; Sander, Chris; Keskin, Derin B.; Wu, Catherine J.; Fraenkel, Ernest; Hacohen, Nir. Dictionary of immune responses to cytokines at single-cell resolution. Nature 625, 377-384 (2024). doi:10.1038/s41586-023-06816-9.

Examples

if (FALSE) { # \dontrun{
references <- PrepareIREA(db = "IREA_NK_cell", species = "Mus_musculus")
result <- RunIREA(c("Isg15", "Ifit3", "Bst2"),
  reference = references[["Mus_musculus"]][["IREA_NK_cell"]],
  analysis = "cell_polarization"
)
IREAPlot(result, plot_type = "radar")
} # }