R/enrichDO.R

In GuangchuangYu/DOSE: Disease Ontology Semantic and Enrichment analysis

##' DO Enrichment Analysis 
##'
##' Given a vector of genes, this function will return the enrichment DO
##' categories with FDR control.
##'
##' @rdname enrichDO
##' @param ont one of "HDO", "HPO" or "MPO".
##' @param organism one of "hsa" and "mmu"
##' @inheritParams enrichNCG
##' @return A \code{enrichResult} instance.
##' @export
##' @seealso \code{\link{enrichResult-class}}
##' @author Guangchuang Yu \url{https://yulab-smu.top}
##' @keywords manip
##' @examples
##'
##'	data(geneList)
##' 	gene = names(geneList)[geneList > 1]
##' 	yy = enrichDO(gene, pvalueCutoff=0.05)
##' 	summary(yy)
##'
enrichDO <- function(gene, ont="HDO",
                     organism = "hsa",
                     pvalueCutoff=0.05,
                     pAdjustMethod="BH",
                     universe,
                     minGSSize = 10,
                     maxGSSize = 500,
                     qvalueCutoff=0.2,
                     readable = FALSE){

    enrichDisease(gene = gene,
                  organism = organism,
                  pvalueCutoff = pvalueCutoff,
                  pAdjustMethod = pAdjustMethod,
                  universe = universe,
                  minGSSize = minGSSize,
                  maxGSSize = maxGSSize,
                  qvalueCutoff = qvalueCutoff,
                  readable = readable,
                  ontology = ont)
}