loadBioplex.RdloadBioplex saves and/or loads the data stored on Bioplex website http://bioplex.hms.harvard.edu/downloadInteractions.php. Depends on the tsv file containing the following columns:
Gene A Gene B Uniprot A Uniprot B Symbol A Symbol B p(Wrong) p(No Interaction) p(Interaction)
loadBioplex(dir = "./", url = "http://bioplex.hms.harvard.edu/data/BioPlex_2.3_interactionList.tsv", uniprot_id = T)
| dir | directory where to save/look for the local copy |
|---|---|
| uniprot_id | If TRUE uses UniprotKB accessions to identify interacting partners. If FALSE uses gene id (ENTREZ gene id) to identify interacting partners. |
loadBioplex saves loadBioplex data to a file, returns the object of class clean_MItab25
loadBioplex("./")#>#> #> ` Object of class clean_MItab27 (molecular interaction data), for query, file, format, databases, date: ` #> [1] "Summary of protein interactions in the BioPlex network following reanalysis of all data from BioPlex 2.0 plus an additional ~1500 unpublished AP-MS experiments: http://bioplex.hms.harvard.edu/data/BioPlex_2.3_interactionList.tsv" #> #> ` view of the $data: ` #> IDs_interactor_A IDs_interactor_B interactor_IDs_databases_A #> 1: A5A3E0 P00813 uniprotkb #> 2: Q07021 Q8N7W2 uniprotkb #> 3: O75096 Q8N7W2 uniprotkb #> 4: P11142 Q6ZMN8 uniprotkb #> 5: Q53FA3 Q6ZMN8 uniprotkb #> --- #> 73887: A6NHX0 Q8WTX7 uniprotkb #> 73888: Q8WTX7 Q9NXC5 uniprotkb #> 73889: Q6PJI9 Q8WTX7 uniprotkb #> 73890: Q8WTX7 Q96S15-2 uniprotkb #> 73891: Q8WTX7 Q96GY0 uniprotkb #> interactor_IDs_databases_B Taxid_interactor_A Taxid_interactor_B #> 1: uniprotkb 9606 9606 #> 2: uniprotkb 9606 9606 #> 3: uniprotkb 9606 9606 #> 4: uniprotkb 9606 9606 #> 5: uniprotkb 9606 9606 #> --- #> 73887: uniprotkb 9606 9606 #> 73888: uniprotkb 9606 9606 #> 73889: uniprotkb 9606 9606 #> 73890: uniprotkb 9606 9606 #> 73891: uniprotkb 9606 9606 #> Publication_Identifiers #> 1: Bioplex|GeneA|100|GeneB|728378|SymbolA|ADA|SymbolB|POTEF|p(Wrong)|7.90248563407152e-10|p(No Interaction)|0.000143448545513807 #> 2: Bioplex|GeneA|222389|GeneB|708|SymbolA|BEND7|SymbolB|C1QBP|p(Wrong)|2.40536303599679e-14|p(No Interaction)|0.00548411916162282 #> 3: Bioplex|GeneA|222389|GeneB|4038|SymbolA|BEND7|SymbolB|LRP4|p(Wrong)|6.18626306238738e-14|p(No Interaction)|0.000167298651560179 #> 4: Bioplex|GeneA|645121|GeneB|3312|SymbolA|CCNI2|SymbolB|HSPA8|p(Wrong)|2.66331806621062e-15|p(No Interaction)|0.0786165996748185 #> 5: Bioplex|GeneA|645121|GeneB|3305|SymbolA|CCNI2|SymbolB|HSPA1L|p(Wrong)|1.26158784283072e-12|p(No Interaction)|0.107220558595753 #> --- #> 73887: Bioplex|GeneA|652968|GeneB|729438|SymbolA|GATSL3|SymbolB|GATSL2|p(Wrong)|8.05266651996511e-10|p(No Interaction)|8.31827807081233e-10 #> 73888: Bioplex|GeneA|652968|GeneB|54468|SymbolA|GATSL3|SymbolB|MIOS|p(Wrong)|7.25737774786179e-10|p(No Interaction)|1.34274929165835e-05 #> 73889: Bioplex|GeneA|652968|GeneB|79726|SymbolA|GATSL3|SymbolB|WDR59|p(Wrong)|1.61686742345196e-15|p(No Interaction)|0.00661319178346156 #> 73890: Bioplex|GeneA|652968|GeneB|84219|SymbolA|GATSL3|SymbolB|WDR24|p(Wrong)|1.85938569410255e-11|p(No Interaction)|6.95242579374724e-06 #> 73891: Bioplex|GeneA|652968|GeneB|51101|SymbolA|GATSL3|SymbolB|FAM164A|p(Wrong)|3.46729696809162e-09|p(No Interaction)|4.13482211503689e-08 #> Confidence_values Host_organisms bait_prey_status_A bait_prey_status_B #> 1: 0.9998566 NA NA NA #> 2: 0.9945159 NA NA NA #> 3: 0.9998327 NA NA NA #> 4: 0.9213834 NA NA NA #> 5: 0.8927794 NA NA NA #> --- #> 73887: 1.0000000 NA NA NA #> 73888: 0.9999866 NA NA NA #> 73889: 0.9933868 NA NA NA #> 73890: 0.9999930 NA NA NA #> 73891: 1.0000000 NA NA NA #> Interaction_detection_methods Interaction_types Interaction_identifiers #> 1: NA NA NA #> 2: NA NA NA #> 3: NA NA NA #> 4: NA NA NA #> 5: NA NA NA #> --- #> 73887: NA NA NA #> 73888: NA NA NA #> 73889: NA NA NA #> 73890: NA NA NA #> 73891: NA NA NA #> Expansion_methods Features_interactor_A Features_interactor_B #> 1: NA NA NA #> 2: NA NA NA #> 3: NA NA NA #> 4: NA NA NA #> 5: NA NA NA #> --- #> 73887: NA NA NA #> 73888: NA NA NA #> 73889: NA NA NA #> 73890: NA NA NA #> 73891: NA NA NA #> Identification_method_participant_A Identification_method_participant_B #> 1: NA NA #> 2: NA NA #> 3: NA NA #> 4: NA NA #> 5: NA NA #> --- #> 73887: NA NA #> 73888: NA NA #> 73889: NA NA #> 73890: NA NA #> 73891: NA NA #> binding_region_A_start binding_region_A_end binding_region_B_start #> 1: NA NA NA #> 2: NA NA NA #> 3: NA NA NA #> 4: NA NA NA #> 5: NA NA NA #> --- #> 73887: NA NA NA #> 73888: NA NA NA #> 73889: NA NA NA #> 73890: NA NA NA #> 73891: NA NA NA #> binding_region_B_end binding_region_A_type binding_region_B_type #> 1: NA NA NA #> 2: NA NA NA #> 3: NA NA NA #> 4: NA NA NA #> 5: NA NA NA #> --- #> 73887: NA NA NA #> 73888: NA NA NA #> 73889: NA NA NA #> 73890: NA NA NA #> 73891: NA NA NA #> pair_id #> 1: A5A3E0|P00813 #> 2: Q07021|Q8N7W2 #> 3: O75096|Q8N7W2 #> 4: P11142|Q6ZMN8 #> 5: Q53FA3|Q6ZMN8 #> --- #> 73887: A6NHX0|Q8WTX7 #> 73888: Q8WTX7|Q9NXC5 #> 73889: Q6PJI9|Q8WTX7 #> 73890: Q8WTX7|Q96S15-2 #> 73891: Q8WTX7|Q96GY0