R/topGODataNew.R

In wolski/topGOUniProt: GO annotation for uniprot

#' create an topGodata object
#'
#' @param selectedSet selectedSet
#' @param backgroundSet backgroundSet
#' @param ontology ontology to use
#' @param description description
#' @param nodeSize nodeSize
#' @param mapping mapping
#' @export
#' @examples
#' library(topGOUniProt)
#' tmp <-uniprotTable2ProteinGOTable(ontology="CC",mapping=getMouseData(PE=1))
#' head(tmp)
#'
#' protID <- unique(tmp[,1])
#'
#' protIDbackground <- unique(tmp[1:200,1])
#' res <- topGODataNew(selectedSet = protID , backgroundSet = protIDbackground, mapping=getMouseData(PE=1),  ontology="BP" )
#' res <- topGODataNew(selectedSet = protID , backgroundSet = protIDbackground,  mapping=getMouseData(PE=1) , ontology="MF")
#' res <- topGODataNew(selectedSet = protID , backgroundSet = protIDbackground,  mapping=getMouseData(PE=1) , ontology="CC")
#'
#' tmp <- getHumanData(PE=1)
#' head(tmp)
#' protIDbackground <- unique(tmp[,"Entry"])
#' length(protIDbackground)
#' protID <- protIDbackground[1:100]
#'
#' res <- topGODataNew(selectedSet = protID , backgroundSet = protIDbackground,  mapping=getHumanData(PE=1) , ontology="BP")
#' res <- topGODataNew(selectedSet = protID , backgroundSet = protIDbackground,  mapping=getHumanData(PE=0) , ontology="MF")
#' res <- topGODataNew(selectedSet = protID , backgroundSet = protIDbackground,  mapping=getHumanData(PE=0) , ontology="CC")
#'
#' summary(res)
#'
topGODataNew <- function( selectedSet ,
                          backgroundSet,
                          mapping,
                          ontology = "BP",
                          description="Simple session" ,
                          nodeSize = 5 )
{
  require(topGO)
  selectfun <- function(x){
    return(x == 1)
  }
  message(ontology , "ontology")
  tmp <- as.numeric(backgroundSet %in% selectedSet)
  names(tmp) <- backgroundSet
  sampleGOdata <- new("topGOdata",
                      description = description,
                      ontology = ontology,
                      allGenes = (tmp),
                      geneSelectionFun = selectfun,
                      nodeSize = nodeSize,
                      annotationFun = annFUN.uniprot,
                      mapping = mapping)
}