import_Omnipath_annotations {OmnipathR} | R Documentation |
imports the annotations stored in Omnipath database from http://omnipathdb.org/annotations
import_Omnipath_annotations( from_cache_file = NULL, select_genes = NULL, filter_databases = NULL, force_full_download = FALSE, ... )
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 |
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. |
A data.frame containing different gene/complex annotations
annotations = import_Omnipath_annotations(select_genes=c("TP53","LMNA"), filter_databases=c("HPA_subcellular"))