PathBank_metabolite_database

Imports the PathBank database (https://pathbank.org/) of metabolites linked to pathways.

Usage

PathBank_metabolite_database(
  version = "primary",
  bfc_path = NULL,
  resource_name = "MetMashR_PathBank",
  ...
)

Arguments

version

(character) PathBank version. Allowed values are limited to the following:

"": The version of the PatchBank database to import. To prevent unecessary downloads BiocFileCache is used to store a local copy.
"complete": The complete PathBank metabolite database.
"primary": The PathBank metabolite database for primary pathways only.

The default is "primary".

bfc_path

(character, NULL) BiocFileCache is used to cache the database locally and prevent unnecessary downloads. If a path is provided then BiocFileCache will use this location. If NULL it will use the default location (see BiocFileCache::BiocFileCache() for details). The default is NULL.

resource_name

(character) The name given to this resource in the cache. (see BiocFileCache::BiocFileCache() for details). The default is "MetMashR_PathBank".

...

Additional slots and values passed to struct_class.

Value

A PathBank_metabolite_database object. This object has no output slots.

Details

This object makes use of functionality from the following packages:

BiocFileCache
httr

Inheritance

A PathBank_metabolite_database object inherits the following struct classes:

PathBank_metabolite_database() ⭢ BiocFileCache_database() ⭢ annotation_database() ⭢ annotation_source() ⭢ struct_class()

References

Shepherd L, Morgan M (2023). BiocFileCache: Manage Files Across Sessions. doi:10.18129/B9.bioc.BiocFileCache https://doi.org/10.18129/B9.bioc.BiocFileCache, R package version 2.10.1, https://bioconductor.org/packages/BiocFileCache.

Wickham H (2023). httr: Tools for Working with URLs and HTTP. R package version 1.4.7, https://CRAN.R-project.org/package=httr.