#' 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)
}
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