interSpeciesInteractome.RdRetrieve interspecies interactions (proteins only or not) for a given pair of taxonomy IDs from a specified database. Interactome can be additionally cleaned and includes only specific information: cleanMITAB
interSpeciesInteractome(MITABdata = NULL, taxid1 = 9606, taxid2 = 10239, database = "imex", format = "tab25", clean = TRUE, protein_only = TRUE, directory = NULL, releaseORdate = NULL, remove_obsolete_id = F)
| MITABdata | object of class "RAW_MItab25" or "RAW_MItab27" (list) containing molecular interaction data as returned by |
|---|---|
| taxid1 | character (1L), taxonomy id of the species which interaction participants should belong to, default is 9606 (which is human) |
| taxid2 | character (1L), taxonomy id of the species which interaction participants should belong to, default is 10239 (which is all viral taxa) |
| database | character (1L), argument for |
| format | character (1L), argument for |
| clean | logical (1L), if TRUE extract specific information using |
| protein_only | logical (1L), if TRUE the interaction participants are restricted to proteins (exclude other types of molecules such as RNA or small molecules), default is TRUE |
| directory | directory where to store the data, if NULL the data is stored in <R-package-library>/PItools/data |
| releaseORdate | character, if data has already been downloaded: which IntAct release or download date to read |
| remove_obsolete_id | logical (1L), remove interactions in which one of the partners is encoded as obsolete UniProtKB accession (ID), not implemented properly: will never finish. |
object of class `input class`_interSpeciesInteractome containing data.table containing molecular interaction data in either of these two formats:
if clean is TRUE: contains columns as described in cleanMITAB;
if clean is FALSE: contains a standard set of columns for MITAB2.5 or MITAB2.7 depending on format;
taxid1 and taxid2 is used to query specified database using PSICQUIC client, only interacting pairs between taxid1 and taxid2 are retured (no interactions within the same species, "(taxidA:taxid1 AND taxidB:taxid2) OR (taxidA:taxid2 AND taxidB:taxid1)").
interSpeciesInteractome can be used to retrive interactome data using PSICQUIC service using queryPSICQUIC, clean and select specific columns using cleanMITAB and filter resulting dataset for protein-protein interaction only. This is the default option.
Alternatively, interSpeciesInteractome can only retrive interactome data using PSICQUIC service without cleaning of filtering.
Another option is to supply MITABdata to be cleaned and filtered
Finally, you can avoid using PSICQUIC service and download data from IntAct ftp by selecting database argument "IntActFTP". This is much faster but larger requires larger download and is more computationally intensive for processing. As of 7.09.2017 "IntActFTP" provides access to DIP data, while "imex" doesn't. If database "IntActFTP" is chosen only MITAB2.7 is available and format is ignored
{ # retrive a full set of human (9606) protein-protein interactions from IMEx databases in MITAB2.5 format, clean and select specific columns interSpecies = interSpeciesInteractome(taxid1 = 9606, taxid2 = 10239, database = "IntActFTP", format = "tab27", clean = TRUE, protein_only = TRUE) # retrive a full set of human (9606) protein-protein interactions from IMEx databases in MITAB2.7 format not using PSICQUIC (using IntAct ftp), clean and select specific columns; save it to the specific directory inside working directory interSpecies = interSpeciesInteractome(taxid1 = 9606, taxid2 = 10239, database = "IntActFTP", format = "tab27", clean = TRUE, protein_only = TRUE, directory = "./data/") }#>#>#>#> 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.#> Warning: Found and resolved improper quoting out-of-sample. First healed line 5839: <<542959 Bpp1virus "BPP-1-like viruses"; BPP-1-like phages; Bpp-1-like viruses; Bppunalikevirus Genus Viruses; dsDNA viruses, no RNA stage; Caudovirales; Podoviridae 10744 >>. If the fields are not quoted (e.g. field separator does not appear within any field), try quote="" to avoid this warning.#> Warning: Found and resolved improper quoting out-of-sample. First healed line 5839: <<542959 Bpp1virus "BPP-1-like viruses"; BPP-1-like phages; Bpp-1-like viruses; Bppunalikevirus Genus Viruses; dsDNA viruses, no RNA stage; Caudovirales; Podoviridae 10744 >>. If the fields are not quoted (e.g. field separator does not appear within any field), try quote="" to avoid this warning.#>#>#>#> 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.#> Warning: Found and resolved improper quoting out-of-sample. First healed line 5839: <<542959 Bpp1virus "BPP-1-like viruses"; BPP-1-like phages; Bpp-1-like viruses; Bppunalikevirus Genus Viruses; dsDNA viruses, no RNA stage; Caudovirales; Podoviridae 10744 >>. If the fields are not quoted (e.g. field separator does not appear within any field), try quote="" to avoid this warning.#> Warning: Found and resolved improper quoting out-of-sample. First healed line 5839: <<542959 Bpp1virus "BPP-1-like viruses"; BPP-1-like phages; Bpp-1-like viruses; Bppunalikevirus Genus Viruses; dsDNA viruses, no RNA stage; Caudovirales; Podoviridae 10744 >>. If the fields are not quoted (e.g. field separator does not appear within any field), try quote="" to avoid this warning.