R/formatTopGO.R

In klarakaleb/roma: R wrapper for the OMA REST API

#' Format the GO annotations data
#'
#' The function to create a list of GO annotations that is compatible with topGO from protein objects in roma
#'
#' @param geneList the list of OmaDB protein objects or a dataframe of ontologies to be included in the analysis - this is where the GO annotations are extracted from.
#' @param format format for the data to be returned in - either 'GO2geneID' or 'geneID2GO'
#' @return a list containing the GO2geneID or geneID2GO information
#' @export
#' @examples
#' geneList = list(getProtein(id='YEAST01'),getProtein(id='YEAST03'))
#' annotations = formatTopGO(geneList,format='geneID2GO')



formatTopGO <- function(geneList, format) {

    if (!(format %in% list("GO2geneID", "geneID2GO"))) {
        stop("Invalid format. Must be either 'GO2geneID' or 'geneID2GO'")
    }

    if (class(geneList) == "data.frame") {

        geneNames <- unique(geneList$entry_nr)
        geneListFormatted <- lapply(geneNames, function(x) geneList[geneList$entry_nr ==
            x, ]$GO_term)

        names(geneListFormatted) <- geneNames

        geneID2GO <- geneListFormatted

    } else {
        geneID2GO <- lapply(geneList, FUN = function(protein) {

            if (startsWith(protein[["gene_ontology"]], "https://")) {
                annotation <- protein$gene_ontology

                if (class(annotation) == "data.frame") {
                  unlist(as.list(annotation[["GO_term"]]))
                } else {
                  annotation
                }
            } else {
                if (class(annotation) == "data.frame") {
                  unlist(as.list(protein[["gene_ontology"]][["GO_term"]]))
                } else {
                  annotation
                }
            }
        })

        names(geneID2GO) <- lapply(geneList, FUN = function(protein) {
            protein$omaid
        })

    }


    if (format == "geneID2GO") {
        return(geneID2GO)
    }
    if (format == "GO2geneID") {
        return(topGO::inverseList(geneID2GO))
    }
}