import_Omnipath_annotations {OmnipathR}R Documentation

Import Omnipath Annotations

Description

imports the annotations stored in Omnipath database from http://omnipathdb.org/annotations

Usage

import_Omnipath_annotations(
  from_cache_file = NULL,
  select_genes = NULL,
  filter_databases = NULL,
  force_full_download = FALSE,
  ...
)

Arguments

from_cache_file

Path to an earlier data file

select_genes

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.

filter_databases

Load the annotations only from these databases. See get_annotation_databases for possible values.

force_full_download

Force the download of the entire annotations dataset. This 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 databases, depending on your interest.

...

Additional arguments.

Value

A data.frame containing different gene/complex annotations

See Also

get_annotation_databases

Examples

annotations = import_Omnipath_annotations(select_genes=c("TP53","LMNA"),
     filter_databases=c("HPA_subcellular"))

[Package OmnipathR version 1.2.1 Index]