import_omnipath_annotations: Imports annotations from OmniPath

In saezlab/OmnipathR: OmniPath web service client and more

Imports annotations from OmniPath

Description

Imports protein annotations about function, localization, expression, structure and other properties of proteins from OmniPath https://omnipathdb.org/annotations. Note: there might be also a few miRNAs annotated; a vast majority of protein complex annotations are inferred from the annotations of the members: if all members carry the same annotation the complex inherits.

Usage

import_omnipath_annotations(
  proteins = NULL,
  resources = NULL,
  wide = FALSE,
  organism = "human",
  genesymbol_resource = NULL,
  ...
)

Arguments

proteins	Vector containing the genes or proteins for whom annotations will be retrieved (UniProt IDs or HGNC Gene Symbols or miRBase IDs). It is also possible to donwload annotations for protein complexes. To do so, write 'COMPLEX:' right before the genesymbols of the genes integrating the complex. Check the vignette for examples.
resources	Load the annotations only from these databases. See get_annotation_resources for possible values.
wide	Convert the annotation table to wide format, which corresponds more or less to the original resource. If the data comes from more than one resource a list of wide tables will be returned. See examples at pivot_annotations.
organism	Character or integer: Name or NCBI Taxonomy ID of one or organisms. The web service currently provides intercell annotations only for human. For other organisms, the data will be translated by orthologous gene pairs from human.
genesymbol_resource	Character: either "uniprot" or "ensembl". The former leaves intact the gene symbols returned by the web service, originally set from UniProt. The latter updates the gene symbols from Ensembl, which uses a slightly different gene symbol standard. In this case a few records will be duplicated, where Ensembl provides ambiguous translation.
...	Additional arguments.

Details

Downloading the full annotations dataset is disabled by default because the size of this data is around 1GB. We recommend to retrieve the annotations for a set of proteins or only from a few resources, depending on your interest. You can always download the full database from https://archive.omnipathdb.org/omnipath_webservice_annotations__recent.tsv using any standard R or readr method.

Value

A data frame containing different gene and complex annotations.

See Also

• get_annotation_databases

• pivot_annotations

Examples

annotations <- import_omnipath_annotations(
    proteins = c('TP53', 'LMNA'),
    resources = c('HPA_subcellular')
)

saezlab/OmnipathR documentation built on July 13, 2024, 6:18 p.m.