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MTox700plus_database

Source: R/MTox700plus_database_class.R
MTox700plus_database.Rd

Imports the MTox700+ database, which is made available under the ODC Attribution License. MTox700+ is a list of toxicologically relevant metabolites derived from publications, public databases and relevant toxicological assays.

Usage

MTox700plus_database(
  version = "latest",
  bfc_path = NULL,
  resource_name = "MetMashR_MTox700plus",
  ...
)

Arguments

version

(character) The version number of the MTox700+ database to import. Available versions are listed here: https://github.com/michabohealthscience/MTox700plus/releases. version should match the tag of the release e.g. "v1.0". For convenience version = "latest" will always retrieve the most recent release. To prevent unecessary downloads BiocFileCache is used to store a local copy. The default is "latest".

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_MTox700plus".

...

Additional slots and values passed to struct_class.

Value

A MTox700plus_database object. This object has no output slots.

Details

This object makes use of functionality from the following packages:

  • BiocFileCache

  • httr

Inheritance

A MTox700plus_database object inherits the following struct classes:

[MTox700plus_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.

Sostare E, Lawson TN, Saunders LR, Colbourne JK, Weber RJM, Sobanski T, Viant MR (2022). "Knowledge-Driven Approaches to Create the MTox700+ Metabolite Panel for Predicting Toxicity." Toxicological Sciences, 186, 208-220. doi:10.1093/toxsci/kfac007 https://doi.org/10.1093/toxsci/kfac007.

Examples

M = MTox700plus_database( version = "v1.0", bfc_path = NULL,
resource_name = "bfc", bfc_fun = function(){}, import_fun =
function(){}, offline = FALSE, tag = character(0), data =
data.frame(id=NA), source = "ANY")