R/GOenrich.R

In Jiahao-Kuang/seqanalyseR: a package to analyse seq data

#' GOenrich
#'
#'Analyse RNA-seq data
#' @param GENE_TO_ENRICH gene list generated by IDchange
#' @param CHANGEtoTYPE type of gene
#' @param SPECIES specie
#' @example
#' GOenrich(GENE_TO_ENRICH,SPECIES)
GOenrich<-function(x,SPECIES){
  species_list<-c("HUMAN","MOUSE","RAT")
  if (!SPECIES%in%species_list) {
    ERRORinSPECIES<-paste("input should be one of",paste(species_list,collapse = ","))
    stop('"SPECIES"', ERRORinSPECIES)
  }
  if (SPECIES=="HUMAN") {
    library("org.Hs.eg.db")
    OrgDb="org.Hs.eg.db"
  }
  if (SPECIES=="MOUSE") {
    library("org.Mn.eg.db")
    OrgDb="org.Mn.eg.db"
  }
  if (SPECIES=="RAT") {
    library("org.Rn.eg.db")
    OrgDb="org.Rn.eg.db"
  }
  library(clusterProfiler)
  GO_readble<-clusterProfiler::enrichGO(x,
                                        OrgDb = OrgDb,
                                        keyType = 'ENTREZID',
                                        ont = 'ALL',
                                        pvalueCutoff = 0.05,#设定p值阈值
                                        qvalueCutoff = 0.05,#设定q值阈值
                                        readable = TRUE)
  return(GO_readble)
}