R/getTopGO.R

In DessimozLab/OmaDB: R wrapper for the OMA REST API

#' Get the topGO Object function
#'
#' The function to create a topGO object containing the GO annotations for the given protein list.
#'
#' @param annotations list of GO annoatations obtained from the formatTopGO()
#' @param foregroundGenes List of identifiers for the foreground genes
#' @param format Format for the data to be returned in - either 'GO2geneID' or 'geneID2GO'
#' @param ontology The ontology for which the enrichment should be done. This
#'        parameter is passed directly to the topGOdata constructor.
#' @return topGO object
#' @export
#' @import topGO
#' @importFrom topGO annFUN.gene2GO
#' @importFrom methods new
#' @examples
#' geneList = list(getProtein(id='YEAST58'),getProtein(id='YEAST00059'))
#' annotations = formatTopGO(geneList,format='geneID2GO')
#' library(topGO)
#' getTopGO(annotations, foregroundGenes = list('YEAST00058'), format = 'geneID2GO', ontology = 'BP')

getTopGO <- function(annotations, format, foregroundGenes, ontology) {

    if (missing(ontology)) {
        stop("You must provide the ontology for which the enrichment should be done.")
    }

    if (missing(annotations) || class(annotations) != "list") {
        stop("You must provide a valid list of annotations.")
    }

    if (missing(format) || !(format %in% list("geneID2GO", "GO2geneID"))) {
        stop("You must provide a valid annotations format.")
    }

    if (missing(foregroundGenes)) {
        stop("You must provide a valid list of genes of interest.")
    }

    if (class(foregroundGenes) == "data.frame") {
        foregroundGenes <- foregroundGenes[["omaid"]]
    }

    geneNames <- names(annotations)
    geneList <- factor(as.integer(geneNames %in% foregroundGenes))
    names(geneList) <- geneNames

    if (format == "geneID2GO") {
        GOdata <- new("topGOdata", ontology = ontology, allGenes = geneList, annot = topGO::annFUN.gene2GO,
            gene2GO = annotations)
    }
    if (format == "GO2geneID") {
        GOdata <- new("topGOdata", ontology = ontology, allGenes = geneList, annot = topGO::annFUN.GO2genes,
            GO2gene = annotations)
    }
    return(GOdata)
}