subsetMITABbyMethod: Filter molecular interactions by interaction detection...

In vitkl/MItools: Protein interaction data tools: retrieving data from IntAct and most other databases using PSICQUIC service

Description

filter molecular interaction data by Interaction_detection_methods and / or participant Identification_method

Usage

subsetMITABbyMethod(MITABdata, Interaction_detection_methods = NULL,
  Identification_method = NULL,
  Identification_method_participant_A = NULL,
  Identification_method_participant_B = NULL,
  ontology_directory = "./", ontology_date = NULL,
  inverse_filter = F)

Arguments

MITABdata	object of any clean_MItab class (the class that contains "clean_MItab" in it's name and is initially produced by MITABdata)
Interaction_detection_methods	character or character vector, Molecular Interaction ontology code for Interaction detection method, such as "MI:0018", default option results in no filtering by Interaction detection method. Details http://purl.obolibrary.org/obo/MI_0001
Identification_method	character or character vector, Molecular Interaction ontology code for Identification method, such as "MI:0433". Applies the same Identification method filter to both participant_A and participant_B. Default option results in no filtering by Identification method. Details http://purl.obolibrary.org/obo/MI_0002
Identification_method_participant_A	character or character vector, Molecular Interaction ontology code for Identification method for participant A, such as "MI:0433", default option results in no filtering by Interaction detection method for this participant. Parameter is ignored if Identification_method specified. Details http://purl.obolibrary.org/obo/MI_0002
Identification_method_participant_B	character or character vector, Molecular Interaction ontology code for Identification method for participant B, such as "MI:0433", default option results in no filtering by Interaction detection method for this participant. Parameter is ignored if Identification_method specified. Details http://purl.obolibrary.org/obo/MI_0002
ontology_directory	where local copy of the MI ontology is stored (if file not found it will be downloaded)
ontology_date	character, such as "2017_08_25", use specific version of ontology (local copy must be present), by default (NULL) download the latest version. The function doesn't require internet access if this argument is provided.
inverse_filter	logical, inverse filtering criteria

Value

object of the same class as MITABdata, a subset of MITABdata that contains interactions for Interaction_detection_methods and / or participant Identification_method

Author(s)

Vitalii Kleshchevnikov

See Also

subsetMITABbyPMIDs), subsetMITABbyID)

Examples

{
# Download all human interaction data
full = fullInteractome(taxid = "9606", database = "IntActFTP",
         clean = TRUE, protein_only = TRUE)

# subset two-hybrid interactions
two_hybrid = subsetMITABbyMethod(MITABdata = full,
               Interaction_detection_methods = "MI:0018")

# subset all interactions but two-hybrid
NOT_two_hybrid = subsetMITABbyMethod(MITABdata = full,
                   Interaction_detection_methods = "MI:0018", inverse_filter = T)

# subset affinity purification - mass spectrometry interactions
AP_MS = subsetMITABbyMethod(MITABdata = full,
               Interaction_detection_methods = "MI:0004",  Identification_method = "MI:0433")
}

vitkl/MItools documentation built on May 29, 2019, 2:55 p.m.