Filter molecular interactions by Pubmed ID

filter molecular interaction data by Pubmed ID of publications

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

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# subset unpublished Vidal group data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# subset both published and unpublished Vidal group data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")
}
#> ... looking for the date of the latest IntAct release ...
#> ... looking for the date of the latest IntAct release ...
#> ... loading local copy ...
#> Warning: Found and resolved improper quoting out-of-sample. First healed line 25383: <<uniprotkb:P16054	uniprotkb:Q05769	intact:EBI-298451	intact:EBI-298933|uniprotkb:Q543K3	psi-mi:kpce_mouse(display_long)|uniprotkb:Prkce(gene name)|psi-mi:Prkce(display_short)|uniprotkb:Pkce(gene name synonym)|uniprotkb:Pkcea(gene name synonym)|uniprotkb:nPKC-epsilon(gene name synonym)	psi-mi:pgh2_mouse(display_long)|uniprotkb:Ptgs2(gene name)|psi-mi:Ptgs2(display_short)|uniprotkb:Cox-2(gene name synonym)|uniprotkb:Cox2(gene name synonym)|uniprotkb:Pghs-b(gene name synonym)|uniprotkb:Tis10(gene na>>. If the fields are not quoted (e.g. field separator does not appear within any field), try quote="" to avoid this warning.