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Load versioned SpaMTP annotation resources

Source: R/DatabaseResources.R
LoadSpaMTPDatabase.Rd

Loads annotation resources bundled with SpaMTP without another data package, a Hub lookup, or a download. Resources are cached for the current R session. A named custom bundle or local RDS directory can be supplied for user-curated workflows.

Usage

LoadSpaMTPDatabase(
  resources = c("chem_props", "source_df", "analyte", "analytehaspathway", "pathway"),
  version = "latest",
  source = c("auto", "bundled", "local"),
  database = NULL,
  local_dir = NULL,
  hub = NULL,
  offline = FALSE,
  refresh = FALSE
)

Arguments

resources

Character vector of resource names. Use SpaMTPDatabaseInfo() to list valid names.

version

Database snapshot version, or "latest" for the bundled snapshot. For local files, declared metadata must match an explicit version.

source

Database source. "auto" uses bundled data unless local_dir is supplied. "bundled" uses installed data; "local" requires local RDS files and never falls back to another source.

database

Optional named list containing the requested resources. When supplied, no Hub lookup is performed.

local_dir

Optional directory containing <resource>.rds files, either directly or in a version-named subdirectory. Without local version metadata, "latest" files are labelled "unversioned".

hub

Retained for call compatibility; must be NULL in this release.

offline

Retained for call compatibility. All resource loading is offline, regardless of this argument.

refresh

If TRUE, bypass SpaMTP's in-session resource cache.

Value

A named list containing the requested resources.

Details

Bundled RaMP 3.0.7 graphs already include corrected interaction labels and directions. Exact affected local or custom topology resources receive a checksum-guarded correction for historical interaction-code and direction recycling. Source labels are retained in source_reaction_type; the resource attribute spamtp_interaction_repair records the correction separately from the original download metadata. Published files are unchanged. See vignette("Pathway_Database_Integration", package = "SpaMTP") for provenance and reproducible build instructions.

Examples

utils::str(formals(LoadSpaMTPDatabase))
#> Dotted pair list of 8
#>  $ resources: language c("chem_props", "source_df", "analyte", "analytehaspathway", "pathway")
#>  $ version  : chr "latest"
#>  $ source   : language c("auto", "bundled", "local")
#>  $ database : NULL
#>  $ local_dir: NULL
#>  $ hub      : NULL
#>  $ offline  : logi FALSE
#>  $ refresh  : logi FALSE
example_database <- list(
  ramp_db_metadata = list(ramp_version = "example")
)
database <- LoadSpaMTPDatabase(
  "ramp_db_metadata",
  database = example_database
)
names(database)
#> [1] "ramp_db_metadata"