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 = get_annotation_databases()
)

Arguments

from_cache_file

path to an earlier data file

select_genes

vector containing the genes for whom annotations will be retrieved (hgnc format). It is also possible to donwload complexes annotations. To do so, write "COMPLEX:" right before the genesymbols of the genes integrating the complex. Check the vignette for examples.

filter_databases

annotations not reported in these databases are removed. See get_annotation_databases for more information.

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"))

[Package OmnipathR version 1.0.1 Index]