R/enrichHPO.r

In YuLab-SMU/DOSE: Disease Ontology Semantic and Enrichment analysis

##' Enrichment analysis based on the DisGeNET (\url{http://www.disgenet.org/})
##'
##' given a vector of genes, this function will return the enrichment NCG
##' categories with FDR control
##'
##'
##' @inheritParams enrichNCG
##' @return A \code{enrichResult} instance
##' @export
##' @references Janet et al. (2015) DisGeNET: a discovery platform for the dynamical exploration of human diseases and their genes. \emph{Database} bav028
##' \url{http://database.oxfordjournals.org/content/2015/bav028.long}
##' @author Erqiang Hu
enrichHPO <- function(gene,
                      pvalueCutoff = 0.05,
                      pAdjustMethod = "BH",
                      universe,
                      minGSSize = 10,
                      maxGSSize = 500,
                      qvalueCutoff = 0.2,
                      readable = FALSE){

    enrichDisease(gene = gene,
                  pvalueCutoff = pvalueCutoff,
                  pAdjustMethod = pAdjustMethod,
                  universe = universe,
                  minGSSize = minGSSize,
                  maxGSSize = maxGSSize,
                  qvalueCutoff = qvalueCutoff,
                  readable = readable,
                  ontology = "HPO")
    
}



#' Get HPO data
#' @noRd 
get_HPO_data <- function() {
    get_dose_data("HPO")
}