## ----set-options, echo=FALSE, cache=FALSE------------------------------------------------------------------- options(width = 110) ## ----installation, eval=FALSE------------------------------------------------------------------------------- # library(devtools) # install_github('saezlab/OmnipathR') ## ----library------------------------------------------------------------------------------------------------ library(OmnipathR) ## ----network------------------------------------------------------------------------------------------------ gri <- import_transcriptional_interactions() gri ## ----network-igraph----------------------------------------------------------------------------------------- gr_graph <- interaction_graph(gri) gr_graph ## ----paths-------------------------------------------------------------------------------------------------- paths <- find_all_paths( graph = gr_graph, start = c('EGFR', 'STAT3'), end = c('AKT1', 'ULK1'), attr = 'name' ) ## ----enzsub------------------------------------------------------------------------------------------------- enz_sub <- import_omnipath_enzsub() enz_sub ## ----enzsub-igraph------------------------------------------------------------------------------------------ es_graph <- enzsub_graph(enz_sub) es_graph ## ----enzsub-signs------------------------------------------------------------------------------------------- es_signed <- get_signed_ptms(enz_sub) ## ----complexes---------------------------------------------------------------------------------------------- cplx <- import_omnipath_complexes() cplx ## ----uniprot-loc-------------------------------------------------------------------------------------------- uniprot_loc <- import_omnipath_annotations( resources = 'UniProt_location', wide = TRUE ) uniprot_loc ## ----uniprot-loc-1------------------------------------------------------------------------------------------ uniprot_loc <- import_omnipath_annotations( resources = 'Uniprot_location', wide = TRUE ) ## ----uniprot-loc-2, error = TRUE---------------------------------------------------------------------------- uniprot_loc <- import_omnipath_annotations( resuorces = 'UniProt_location', wide = TRUE ) ## ----uniprot-loc-3------------------------------------------------------------------------------------------ uniprot_loc <- import_omnipath_annotations( resource = 'UniProt_location', wide = TRUE ) ## ----hpa-tissue--------------------------------------------------------------------------------------------- hpa_tissue <- import_omnipath_annotations( resources = 'HPA_tissue', wide = TRUE, # Limiting to a handful of proteins for a faster vignette build: proteins = c('DLL1', 'MEIS2', 'PHOX2A', 'BACH1', 'KLF11', 'FOXO3', 'MEFV') ) hpa_tissue ## ----slk-pathway-------------------------------------------------------------------------------------------- slk_pathw <- import_omnipath_annotations( resources = 'SignaLink_pathway', wide = TRUE ) slk_pathw ## ----annotate-network--------------------------------------------------------------------------------------- network <- import_omnipath_interactions() network_slk_pw <- annotated_network(network, 'SignaLink_pathway') network_slk_pw ## ----intercell---------------------------------------------------------------------------------------------- ic <- import_omnipath_intercell() ic ## ----intercell-network-------------------------------------------------------------------------------------- icn <- import_intercell_network(high_confidence = TRUE) icn ## ----intercell-filter--------------------------------------------------------------------------------------- icn <- import_intercell_network() icn_hc <- filter_intercell_network( icn, ligand_receptor = TRUE, consensus_percentile = 30, loc_consensus_percentile = 50, simplify = TRUE ) ## ----annot-res---------------------------------------------------------------------------------------------- get_annotation_resources() ## ----intercell-cat------------------------------------------------------------------------------------------ get_intercell_generic_categories() # get_intercell_categories() # this would show also the specific categories ## ----id-translate-vector------------------------------------------------------------------------------------ d <- data.frame(uniprot_id = c('P00533', 'Q9ULV1', 'P43897', 'Q9Y2P5')) d <- translate_ids( d, uniprot_id = uniprot, # the source ID type and column name genesymbol # the target ID type using OmniPath's notation ) d ## ----id-translate-df, eval = FALSE-------------------------------------------------------------------------- # network <- import_omnipath_interactions() # network <- translate_ids( # network, # source = uniprot_id, # source_entrez = entrez # ) # network <- translate_ids( # network, # target = uniprot_id, # target_entrez = entrez # ) ## ----go----------------------------------------------------------------------------------------------------- go <- go_ontology_download() go$rel_tbl_c2p ## ----go-graph----------------------------------------------------------------------------------------------- go_graph <- relations_table_to_graph(go$rel_tbl_c2p) go_graph ## ----go-name------------------------------------------------------------------------------------------------ ontology_ensure_name('GO:0000022') ## ----cache-------------------------------------------------------------------------------------------------- omnipath_cache_search('dorothea') ## ----license, eval = FALSE---------------------------------------------------------------------------------- # options(omnipath.license = 'commercial') ## ----sessionInfo, echo=FALSE-------------------------------------------------------------------------------- sessionInfo()