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PathBank_metabolite_database

Source: R/PathBank_metabolite_database_class.R
PathBank_metabolite_database.Rd

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 (2024). BiocFileCache: Manage Files Across Sessions. R package version 2.10.2.

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

Wishart, S D, Li, Carin, Marcu, Ana, Badran, Hasan, Pon, Allison, Budinski, Zachary, Patron, Jonas, Lipton, Debra, Cao, Xuan, Oler, Eponine, Li, Krissa, Paccoud, Maïlys, Hong, Chelsea, Guo, C A, Chan, Christopher, Wei, William, Ramirez-Gaona, Miguel (2019). "PathBank: a comprehensive pathway database for model organisms." Nucleic Acids Research, 48, D470-D478. doi:10.1093/nar/gkz861 https://doi.org/10.1093/nar/gkz861.

Examples

M <- PathBank_metabolite_database(
        version = "primary",
        bfc_path = NULL,
        resource_name = "bfc",
        bfc_fun = function(){},
        import_fun = function(){},
        offline = FALSE,
        tag = character(0),
        data = data.frame(),
        source = "ANY")