R/makeAnnot.R

In hurlab/RichR: Function Enrichment analysis and Network construction

##' build annotation database
##' @name buildAnnot
##' @rdname buildAnnot-methods
##' @title make annotation database
##' @param species species for the annotation
##' @param keytype key type export
##' @param anntype annotation type
##' @param bulitin use default database(TRUE or FALSE)
##' @param OP BP,CC,MF default use all
##' @examples
##' \dontrun{
##' annot<-buildAnnot(species="human",keytype="ENTREZID",anntype="GO",bulitin=TRUE)
##' }
##' @export
##' @author Kai Guo
buildAnnot<-function(species="human",keytype="SYMBOL",anntype="GO",builtin=TRUE,OP=NULL){
  if(anntype=="GO"){
     annot <- .makeGOdata(species=species,keytype=keytype,OP=OP)
  }
  if(anntype=="KEGG"){
    annot <- .makeKOdata(species=species,keytype=keytype,builtin=builtin)
  }
  if(anntype=="Reactome"){
    annot <- .makeROdata(species=species,keytype=keytype)
  }
  if(anntype=="KEGGM"){
    annot <- .makeKOMdata(species=species,keytype=keytype)
  }
  result<-new("Annot",
              species = species,
              anntype = anntype,
              keytype = keytype,
              annot = annot

  )
}
#' make GO annotation data function
#' @importFrom AnnotationDbi keys
#' @param species you can check the support species by using showData()
#' @param keytype the gene ID type
#' @param OP BP,CC,MF default use all
#' @importFrom dplyr distinct
#' @author Kai Guo
.makeGOdata<-function(species="human",keytype="ENTREZID",OP=NULL){
  dbname<-.getdbname(species);
  if (!require(dbname,character.only=TRUE)){
    if(!require("BiocManager",character.only=TRUE)){
      install.packages("BiocManager")
    }else{
      BiocManager::install(dbname)
    }
  }else{
    suppressMessages(requireNamespace(dbname,character.only = T,quietly = T))
  }
  dbname<-eval(parse(text=dbname))
  GO_FILE<-AnnotationDbi::select(dbname,keys=keys(dbname,keytype=keytype),keytype=keytype,columns=c("GOALL","ONTOLOGYALL"))
  colnames(GO_FILE)[1]<-"GeneID"
  #GO_FILE<-distinct_(GO_FILE,~GeneID, ~GOALL, ~ONTOLOGYALL)
  GO_FILE <- distinct(GO_FILE[,c('GeneID','GOALL','ONTOLOGYALL')])
  annot <- getann("GO")
  GO_FILE$Annot <- annot[GO_FILE[,2],"annotation"]
  if(!is.null(OP)){
    GO_FILE<-GO_FILE[GO_FILE$ONTOLOGYALL==OP,]
  }
  return(GO_FILE)
}
#' make KEGG annotation data function
#' @importFrom AnnotationDbi keys
#' @importFrom KEGGREST keggLink
#' @param species you can check the support species by using showData()
#' @param keytype the gene ID type
#' @author Kai Guo
.makeKOdata<-function(species="human",keytype="ENTREZID",builtin=TRUE){
  dbname<-.getdbname(species=species);
  if(builtin==TRUE){
    # suppressMessages(require(AnnotationDbi))
    #  sel<-AnnotationDbi::select
    if (!require(dbname,character.only=TRUE)){
      if(!require("BiocManager",character.only=TRUE)){
        install.packages("BiocManager")
      }else{
        BiocManager::install(dbname)
      }
    }else{
      suppressMessages(requireNamespace(dbname))
    }
    dbname<-eval(parse(text=dbname))
    KO_FILE=AnnotationDbi::select(dbname,keys=keys(dbname,keytype=keytype),keytype=keytype,columns="PATH")
    KO_FILE<-na.omit(KO_FILE)
  }else{
    spe=.getspeices(species)
    tmp<-keggLink("pathway",spe)
    tmp<-substr(tmp,9,13)
    names(tmp)<-sub('.*:','',names(tmp))
    tmp<-vec_to_df(tmp,name=c(keytype,"PATH"))
    if(keytype!="ENTREZID"){
      tmp[,1]<-idconvert(species,keys=tmp[,1],fkeytype = "ENTREZID",tkeytype = keytype)
      tmp<-na.omit(tmp)
    }
    KO_FILE=tmp
  }
  annot<-getann("KEGG")
  KO_FILE[,1]<-as.vector(KO_FILE[,1])
  KO_FILE[,2]<-as.vector(KO_FILE[,2])
  KO_FILE$Annot<-annot[KO_FILE[,2],"annotation"]
  colnames(KO_FILE)[1]<-"GeneID"
  return(KO_FILE)
}

##' Download database from Msigdb and prepare for enrichment analysis
##' @name buildMSIGDB
##' @importFrom msigdbr msigdbr
##' @importFrom dplyr filter
##' @importFrom dplyr select
##' @importFrom rlang sym
##' @importFrom magrittr %>%
##' @param species the species for query
##' @param keytype the gene ID type
##' @param anntype anntotaion type of  gene set (GO,BP,CC,MF,KEGG,REACTOME,
##' BIOCARTA,HALLMARK)
##' @examples
##' \dontrun{
##' hsamsi<-buildMSIGDB(species = "human", keytype = "SYMBOL", anntype = "GO")
##' }
##' @export
##' @author Kai Guo
buildMSIGDB<-function(species="human",keytype="SYMBOL",anntype="GO"){
  flag <- 0
  anntypes <- NULL
  if(!is.null(anntype)){
    if(anntype=="HALLMARK"){
        category <- "H"
        anntype <- ""
    }
    if(anntype == "CGP"){
      category <- "C2"
    }
    if(anntype == "CP"){
      category <- "C2"
    }
    if(anntype == "KEGG"){
      anntypes <- "CP:KEGG"
      category <- "C2"
    }
    if(anntype == "REACTOME"){
      anntypes <- "CP:REACTOME"
      category <- "C2"
    }
    if(anntype == "BIOCARTA"){
      anntypes <- "CP:BIOCARTA"
      category <- "C2"
    }
    if(anntype == "MIR"){
      category <- "C3"
    }
    if(anntype == "TFT"){
      category <- "C3"
    }
    if(anntype == "CGN"){
      category == "C4"
    }
    if(anntype == "CM"){
      category <- "C4"
    }
    if(anntype == "GO"){
      category <- "C5"
    }
    if(anntype == "BP"){
      anntypes <- "GO:BP"
      category <- "C5"
    }
    if(anntype == "CC"){
      anntypes <- "GO:CC"
      category <- "C5"
    }
    if(anntype == "MF"){
      anntypes <- "GO:MF"
      category <- "C5"
    }
  }
  mspe<-.getmsig(species)
  if(is.null(mspe)){
    stop(cat("can't find support species!\n"))
  }
  if(keytype == "SYMBOL"){
    key = "gene_symbol"
  }else if(keytype == "ENTREZID"){
    key = "entrez_gene"
  }else{
    key = "entrez_gene"
    flag = 1
  }
  cat("Downloading msigdb datasets ...\n")
  res <- msigdbr(species = mspe)
  res <- subset(res, gs_cat == category)
  if(!is.null(anntypes)){
    res <- subset(res, gs_subcat == anntypes)
  }
  if(anntype%in%c("GO", "BP", "CC", "MF")){
    res <- res[, c(key, "gs_exact_source", "gs_name")]
    res <- as.data.frame(res)
    colnames(res) <- c("GeneID","GOALL","Annot")
    res$Annot <- sub('.*@','',sub('_','@',res$Annot))
  }else if(anntype == "KEGG"){
    res <- res[,c(key,"gs_exact_source","gs_name")]
    res<-as.data.frame(res)
    colnames(res)<-c("GeneID","PATH","Annot")
    res$PATH<-substr(res$PATH,4,8)
  }else{
    res<-res[,c(key,"gs_name")]
    res<-as.data.frame(res)
    colnames(res)<-c("GeneID","Term")
    res$Term<-sub('.*@','',sub('_','@',res$Term))
    res$Annot<-res[,2]
  }
  if(flag==1){
    res[,1]<-idconvert(species, keys=res[,1], fkeytype="ENTREZID",
                      tkeytype=keytype)
    res<-na.omit(res)
  }
  result<-new("Annot",
              species = species,
              anntype = anntype,
              keytype = keytype,
              annot = res)
  return(result)
}

#' make Reactome annotation data function
#' @importFrom AnnotationDbi as.list
#' @importFrom dplyr left_join
#' @param species you can check the supported species by using showAvailableRO
#' @param keytype key type export
#' @author Kai Guo
.makeROdata<-function(species="human",keytype="SYMBOL"){
  dbname<-.getrodbname(species=species);
  if (!require("reactome.db",character.only=TRUE)){
    if(!require("BiocManager",character.only=TRUE)){
      install.packages("BiocManager")
    }else{
      BiocManager::install("reactome.db")
    }
  }else{
    suppressMessages(require("reactome.db",character.only = T,quietly = T))
  }
  dbname=sapply(strsplit(dbname,"_"),'[[',1)
  lhs<-as.list(reactomePATHNAME2ID)
  lhs<-lhs[grep(dbname,names(lhs))]
  roid<-as.list(reactomePATHID2EXTID)[unique(as.vector(unlist(lhs)))]
  roid<-lapply(roid, function(x)unique(x))
  roid<-data.frame("GeneID"=unlist(roid),"Term"=rep(names(roid),times=lapply(roid, length)),row.names=NULL)
  ll<-lapply(lhs,function(x)unique(x))
  roan<-data.frame("Term"=unlist(ll),"Annot"=rep(names(ll),times=lapply(ll,length)),row.names=NULL)
  roan$Annot<-sub('.*@ ','',sub(':','@',roan$Annot))
  res<-left_join(roid,roan,by=c("Term"="Term"))
  if(keytype!="ENTREZID"){
    keys = idconvert(species = species,keys = res$GeneID,fkeytype = "ENTREZID",tkeytype = keytype)
    res$GeneID = keys
    res <- na.omit(res)
  }
  return(res[,c(1,3)])
}

###
#' make KEGG module annotation data function
#' @importFrom AnnotationDbi keys
#' @importFrom KEGGREST keggLink
#' @param species you can check the support species by using showData()
#' @param keytype the gene ID type
#' @author Kai Guo
.makeKOMdata<-function(species="human",keytype="ENTREZID",builtin=TRUE){
    spe=.getspeices(species)
    tmp<-keggLink("module",spe)
    tmp<-substr(tmp,8,13)
    names(tmp)<-sub('.*:','',names(tmp))
    tmp<-vec_to_df(tmp,name=c(keytype,"Module"))
    if(keytype!="ENTREZID"){
      tmp[,1]<-idconvert(species,keys=tmp[,1],fkeytype = "ENTREZID",tkeytype = keytype)
      tmp<-na.omit(tmp)
    }
    MO_FILE=tmp
    annot<-.get_kgm.data()
    MO_FILE[,1]<-as.vector(MO_FILE[,1])
    MO_FILE[,2]<-as.vector(MO_FILE[,2])
    MO_FILE$Annot<-annot[MO_FILE[,2],"annotation"]
    colnames(MO_FILE)[1]<-"GeneID"
    return(MO_FILE)
}