Function reference • PItools

All functions
`MITABregionFeature()`	Extract binding region feature from cleaned MITAB2.7
`browseMIontology()`	browse Molecular Interaction ontology
`cleanMITAB()`	Process molecular interaction data in MITAB 2.5 or 2.7 formats
`cleanMITAB25()`	`cleanMITAB` extracts and cleans a set of columns of MITAB2.5
`cleanMITAB27()`	`cleanMITAB` extracts and cleans a set of columns of MITAB2.7
`edgelist2degree_slow()`	find the degree for each protein given cleaned molecular interaction data
`edgelist2degreeFreq()`	Find the degree distribution given edgelist (pair_id) and a list of proteins which degrees matter
`extractInteractors()` `uniqueNinteractions()` `uniqueNinteractors()`	Subset MITAB to retrieve interactors, the number of interactions ot interactors
`fullInteractome()`	Retrieve interactome (proteins only or not) of a given taxonomic species
`humanViralDegree()`	Compare viral and human protein degree distribution, filter by interaction detection method or PMIDs
`interSpeciesInteractome()`	Retrieve interspecies interactions (proteins only or not) for a given pair of taxonomy IDs
`interactorFeatureTypes()`	discover types of interactor features in MITAB 2.7
`lastIntActRelease()`	last IntAct (all IMEx databases) release
`loadAllIDProteins()`	load the list of all protein ID in UniProtKB
`loadBioplex()`	load Bioplex data
`loadHumanViralPPI()`	load human-human, human-viral and viral-viral PPI data from IntActFTP
`loadIntActFTP()`	load all data from IntAct ftp
`loadMIontology()`	load Molecular Interaction ontology
`loadTaxIDAllLower()`	load all lower taxonomy ID (all descendants)
`loadTaxIDProteins()`	load the list of all proteins for given taxonomy ID (any level)
`queryPSICQUIC()`	Use PSICQUIC to query for molecular interactions (using MIQL, specifying database and output format)
`queryPSICQUICrlib()`	download PSICQUIC query search result (only IMEx databases) to R library - queryPSICQUIC package - data directory
`randomInteractome()`	Retrieve molecular interactions for the random set of proteins (of a particular taxon)
`readInteractome()`	read Interactome into data.table
`removeInteractionNoFASTA()`	Remove interactions if one participant doesn't have FASTA sequence
`removeInteractionObsoleteID()`	Remove interactions if one participant has obsolete Uniprot accession (ID)
`removeSelfLoops()`	Remove self loops (self-interactions)
`reorderMITAB25()`	`reorderMITAB25` reorders interacting molecules in a pair (and all the corresponding columns) according to order provided in IDs_A_order and IDs_B_order columns (latter are deleted)
`reorderMITAB27()`	`reorderMITAB27` reorders interacting molecules in a pair (and all the corresponding columns) according to order provided in IDs_A_order and IDs_B_order columns (latter are deleted)
`subsetMITABbyID()`	Retrieve interactions for a list of interactors (given data table, not using webservice)
`subsetMITABbyMethod()`	Filter molecular interactions by interaction detection methods and / or participant identification method
`subsetMITABbyPMIDs()`	Filter molecular interactions by Pubmed ID

Reference

All functions

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