R/Genesets-loadGo.R

In MIGSA: Massive and Integrative Gene Set Analysis

#' Creates a GeneSetCollection object using the Gene Ontology data base
#'
#' \code{loadGo} creates a GeneSetCollection object from the data present at
#' the Gene Ontology data base (org.Hs.eg.db R package).
#'
#' @param ontology character indicating which ontology must be loaded.
#' Must be one of BP, MF or CC.
#'
#' @return A GeneSetCollection object  (Genes are with their EntrezGene ID).
#'
#' @docType methods
#' @name loadGo
#' @rdname Genesets-loadGo
#' @seealso \code{\link{as.Genesets}}
#' @seealso \code{\link{Genesets-enrichr}}
#' @seealso \code{\link{geneSetsFromFile}}
#'
#' @exportMethod loadGo
setGeneric(name = "loadGo", def = function(ontology) {
  standardGeneric("loadGo")
})

#' @rdname Genesets-loadGo
#' @aliases loadGo,character-method
#'
#' @importFrom AnnotationDbi as.list mappedkeys Ontology Term
#' @importFrom GSEABase GOCollection GeneSet EntrezIdentifier GeneSetCollection
#' @importFrom org.Hs.eg.db org.Hs.egGO2ALLEGS
#' @examples
#' ## Lets load the Cellular Components gene sets from the Gene Ontology.
#' ccGSets <- loadGo("CC")
setMethod(
  f = "loadGo",
  signature = c("character"),
  definition = function(ontology) {
    ontology <- toupper(ontology)
    if (!ontology %in% c("BP", "CC", "MF")) {
      stop("Ontology must be one of: 'BP', 'CC', 'MF'.")
    }

    # download GO gene sets
    # org.Hs.egGO is an R object that provides mappings between entrez
    # gene identifiers and the GO identifiers that they are directly
    # associated with
    # go <- org.Hs.egGO;

    # org.Hs.egGO2ALLEGS is an R object that provides mappings between
    # a given GO identifier and all of the Entrez Gene identifiers
    # annotated at that GO term OR TO ONE OF ITS CHILD NODES
    go <- org.Hs.egGO2ALLEGS
    goIds <- mappedkeys(go)

    # filter the desired ontology
    ontologies <- Ontology(goIds)
    go <- go[!is.na(ontologies) & ontologies == ontology]
    go <- as.list(go)
    go <- lapply(go, unique)

    goCollection <- GOCollection(
      ontology = ontology,
      evidenceCode = as.character(NA)
    )

    terms <- Term(names(go))
    gsets <- lapply(seq_along(go), function(i) {
      gset <- GeneSet(go[[i]],
        setIdentifier = terms[[i]],
        setName = names(go)[[i]],
        geneIdType = EntrezIdentifier(),
        collectionType = goCollection
      )

      return(gset)
    })

    gsetsColl <- GeneSetCollection(gsets)
    return(gsetsColl)
  }
)