subsetMITABbyPMIDs: Filter molecular interactions by Pubmed ID

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

Description

filter molecular interaction data by Pubmed ID of publications

Usage

subsetMITABbyPMIDs(MITABdata, PMIDs = 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 cleanMITAB)
PMIDs	character or character vector, return only interactions reported by these Pubmed IDs
inverse_filter	logical, inverse filtering criteria

Value

return only interactions reported by PMIDs

Author(s)

Vitalii Kleshchevnikov

See Also

subsetMITABbyMethod), subsetMITABbyID)

Examples

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

# subset unpublished Vidal group data
Vidal = subsetMITABbyPMIDs(MITABdata = full,
               PMIDs = "unassigned1304")

# subset both published and unpublished Vidal group data
Vidal_all = subsetMITABbyPMIDs(MITABdata = full,
               PMIDs = c("25416956", "unassigned1304"))

# subset Mattias Mann 2015 paper data
Mann = subsetMITABbyPMIDs(MITABdata = full,
               PMIDs = "26496610")
}

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