graphSpeciesConverter: maps one type of grap onto another

In RpsiXML: R interface to PSI-MI 2.5 files

Description

The graphConverter function takes a graphNEL object, along with some information about what species that graphNEL is from and what species you wish to convert it into, and then uses the mappings in the inparanoid packages to convert that graph into an equivalent graph from the other species. The hyperGraphConverter performs the same service for either an incidence matrix or a Hypergraph.

Usage

  graphConverter(graph, srcSpecies, destSpecies,
    srcIDType, destIDType, keepMultGeneMatches=FALSE,
    keepMultProtMatches=FALSE)
  hyperGraphConverter(graph, srcSpecies, destSpecies, srcIDType,
    destIDType, mapCols=FALSE, keepMultGeneMatches=FALSE,
    keepMultProtMatches=FALSE)

Arguments

graph	If calling graphConverter. then this is a graphNEL object. Otherwise, it will be an incidence matrix or a hyperGraph
srcSpecies	The original source species in in paranoid format. In other words, the 3 letters of the genus followed by 2 letters of the species in all caps. Ie. 'HOMSA' is for Homo sapiens etc.
destSpecies	the destination species in inparanoid format
srcIDType	The source ID type written exactly as it would be used in a mapping name for an eg package. So for example, 'UNIPROT' is how the uniprot mappings are always written, so we keep that convention here.
destIDType	the destination ID, written the same way as you would write the srcIDType.
mapCols	For hyperGraphConverter set to true if the cols are gene names so that they too will be mapped.
keepMultGeneMatches	Do you want to try and keep the 1st ID in those ambiguous cases where more than one protein is suggested? (You probably want to filter them out - hence the default is FALSE)
keepMultProtMatches	Do you want to try and keep the 1st ID in those ambiguous cases where more than one protein is suggested? (default = FALSE)

Value

A graphNEL containing as many nodes as it was possible to find matches for.

Author(s)

Marc Carlson

Examples

  library(AnnotationDbi)
  directory <- system.file("/extdata/psi25files",
                           package="RpsiXML")
  mintXML <- file.path(directory, 
                       "mint_200711_test.xml")
  mintGraph <- separateXMLDataByExpt(xmlFiles=mintXML, 
                                     psimi25source = MINT.PSIMI25, 
                                     type = "indirect", 
                                     directed=TRUE, 
                                     abstract=FALSE)

#
#  if(require("hom.Mm.inp.db") & require("org.Mm.eg.db")) {
#    newGraph = graphConverter(mintGraph[[1]], "MUSMU", "HOMSA")
#  }

  ##Get a hypergraph
  xmlDir <- system.file("/extdata/psi25files",package="RpsiXML")
  intactComplexxml <- file.path(xmlDir,"intact_complexSample.xml")
  hyperGraph <- buildPCHypergraph(intactComplexxml, INTACT.PSIMI25)

#  if(require("hom.Hs.inp.db")) {
#  ##Convert it
#  newHyper = hyperGraphConverter(hyperGraph, "HOMSA", "MUSMU", "UNIPROT",
#  "UNIPROT")
#  }

  ##Get a incidence matrix from ScISI
  if(require(ScISI))
    data(ScISIC)
#   if(require("org.Sc.eg.db")) {
#     ##Convert it
#     newScISIC = hyperGraphConverter(ScISIC, "SACCE", "MUSMU",
#                 srcIDType="ORF", destIDType = "EG")
#    }

RpsiXML documentation built on Nov. 8, 2020, 6:02 p.m.