addReference: Add reference species

Description

Adds reference species to an object from the class Path2PPI.

Usage

addReference(path2ppi, taxName, taxId, proteins, irefindex, homologs)

Arguments

path2ppi

An object of the class Path2PPI.

taxName

A character string giving the taxonomy name.

taxId

A character string giving the taxonomy identifier.

proteins

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.

irefindex

Either a data frame, representing the iRefIndex table of the current reference species, e.g. loaded previously via read.table, or the corresponding file name of the iRefIndex file.

homologs

Either a data frame representing the results of the BLAST search (e.g. loaded previously via read.table) or the corresponding file name of the BLAST result file.

Value

An object from the class Path2PPI with attached reference species.

Details

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. showReferences)

Examples

Run this code

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