wppi_data: Database knowledge for wppi

In AnaGalhoz37/wppi: Weighting protein-protein interactions

Database knowledge for wppi

Description

Retrieves the database knowledge necessary for WPPI directly from the databases. The databases used here are the Human Phenotype Ontology (HPO, https://hpo.jax.org/app/), Gene Ontology (GO, http://geneontology.org/) and OmniPath (https://omnipathdb.org/). The downloads carried out by the OmnipathR package and data required by wppi are extracted from each table.

Usage

wppi_data(
  GO_slim = NULL,
  GO_aspects = c("C", "F", "P"),
  GO_organism = "human",
  ...
)

Arguments

GO_slim	Character: use a GO subset (slim). If NULL, the full GO is used. The most often used slim is called "generic". For a list of available slims see OmnipathR::go_annot_slim.
GO_aspects	Character vector with the single letter codes of the gene ontology aspects to use. By default all three aspects are used. The aspects are "C": cellular component, "F": molecular function and "P" biological process.
GO_organism	Character: name of the organism for GO annotations.
...	Passed to OmnipathR::import_post_translational_interactions. With these options you can customize the network retrieved from OmniPath.

Details

If you use a GO subset (slim), building it at the first time might take around 20 minutes. The result is saved into the cache so next time loading the data from there is really quick. Gene Ontology annotations are available for a few other organisms apart from human. The currently supported organisms are "chicken", "cow", "dog", "human", "pig" and "uniprot_all". If you disable HPO_annot you can use wppi to score PPI networks other than human.

Value

A list of data frames (tibbles) with database knowledge from HPO, GO and OmniPath.

See Also

• wppi_go_data

• wppi_hpo_data

• wppi_omnipath_data

Examples

# Download all data
data_wppi <- wppi_data()
# OmniPath
omnipath_data <- data_wppi$omnipath
# HPO
HPO_data <- data_wppi$hpo
# GO
GO_data <- data_wppi$go

AnaGalhoz37/wppi documentation built on Nov. 8, 2022, 7:47 a.m.