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 = get_annotation_databases() )
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 |
A data.frame containing different gene/complex annotations
annotations = import_Omnipath_annotations(select_genes=c("TP53","LMNA"), filter_databases=c("HPA"))