Adds reference species to an object from the class
addReference(path2ppi, taxName, taxId, proteins, irefindex, homologs)
An object of the class
A character string giving the taxonomy name.
A character string giving the taxonomy identifier.
Either a character vector with the identifiers of the proteins which are involved in the corresponding pathway or a character vector with the protein names or aliases, respectively, named by the protein identifiers.
Either a data frame, representing the iRefIndex table of the current reference
species, e.g. loaded previously via
Either a data frame representing the results of the BLAST search (e.g. loaded
This method searches for all relevant interactions in the data frame or file
defined in iRefIndex. There are different and often ambiguous protein
identifiers defined in an iRefIndex file, and the putative "major" identifiers
are not necessarily those defined in the corresponding "major" columns "uidA"
and "uidB". Furthermore, iRefIndex also contains protein complexes. Hence,
Path2PPI applies an advanced search algorithm to automatically find
relevant interactions associated with the pathway or the proteins of interest,
respectively. The user does not have to predefine the identifiers types
(Uniprot, Swissprot, Ensemble etc.), since these types are often unambiguously
assigned. The algorithm searches for each identifier in 10 columns where any
type of identifier or accession number is defined ("uidA", "altA",
"OriginalReferenceA", "FinalReferenceA", "aliasA", "uidB", "altB",
"OriginalReferenceB", "FinalReferenceB" and "aliasB"). Additionally, it
searches for each complex which contains one or more of the predefined
proteins. Subsequently, each homologous relationship which is not relevant for
the previously found interactions is declined. The results of these searches
are centralized in the
Path2PPI object and can be visualized using the
appropriate methods (e.g.
An object from the class
Path2PPI with attached reference species.
Oliver Philipp [email protected]
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data(ai) #Load test data set ppi <- Path2PPI("Autophagy induction", "Podospora anserina", "5145") ppi ppi <- addReference(ppi, "Homo sapiens", "9606", human.ai.proteins, human.ai.irefindex, pa2human.ai.homologs) ppi <- addReference(ppi, "Saccharomyces cerevisiae (S288c)", "559292", yeast.ai.proteins, yeast.ai.irefindex, pa2yeast.ai.homologs) ppi
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