Load bundled or user-supplied Alert System pathways — LoadAlertSystemPathways • compact

Lookup order is: an explicitly supplied file/directory, the installed package's inst/extdata, and—only when allowed—a GitHub fallback.

Usage

LoadAlertSystemPathways(
  path = NULL,
  genetype = c("mouse", "human"),
  database = "MSigDBhallmark",
  package = "compact",
  allow_download = TRUE,
  github_base = paste0("https://raw.githubusercontent.com/smorabit/compact/",
    "main/inst/extdata"),
  verbose = TRUE
)

Arguments

path: Optional .rds file or directory containing the expected file.
genetype: Either "mouse" or "human".
database: Filename prefix; default "MSigDBhallmark".
package: Package containing bundled pathway files.
allow_download: Permit the GitHub fallback when no local/package file exists.
github_base: Base raw-content URL used for the optional fallback.
verbose: Whether to report the selected source.

Value

A validated named list of pathway gene vectors.