R/enrichGOGroups.R

In nicohuttmann/htmnanalysis: Analysis of Omics Data

#' GO term enrichment using Fisher's exact test
#'
#' @param sigGenes either vector of genes of interest or numeric vector containing all genes
#' @param allGenes background of genes
#' @param annotations data base containing all annotations
#' @param inverse inverse enrichment
#' @param ontology which ontology to be used (CC, BP, MF)
#' @param nodeSize minimum node size
#' @param save should result table be saved
#' @param name name
#' @param destination where to save
#' @param view view tables
#' @param print should a graphical output be printed
#'
#' @return
#' @export
#'
#' @import topGO
#'
enrichGOGroups <- function(sigGenes, annotations = info[["annotations"]], inverse = F, ontology = "CC", nodeSize = 10, save = F, name, destination, view = T, print = F) {


  groups <- unique(sigGenes)

  results <- list()

  for(group in groups) {



    genes <- as.numeric(sigGenes == group)

    if(inverse) {
      genes <- as.numeric(sigGenes != group)
    }

    names(genes) <- names(sigGenes)



    GOdata <- new("topGOdata",
                  ontology = ontology,
                  allGenes = as.factor(genes),
                  nodeSize = nodeSize,
                  annot = annFUN.gene2GO,
                  gene2GO = annotations[names(genes)])


    test.stat <- new("classicCount", testStatistic = GOFisherTest, name = "Fisher test")

    resultFisher <- getSigGroups(GOdata, test.stat)

    allRes <- GenTable(GOdata,
                       classic = resultFisher,
                       orderBy = "classic",
                       topNodes = 20)

    allRes$proteins <- NA
    allRes$genes <- NA
    allRes$names <- NA

    for(i in 1:nrow(allRes)) {
      p <- intersect(sigGenes, getALLProteins(allRes[i, 1], annotationDB = info[["annotations"]]))
      allRes$proteins[i] <- paste(p, collapse = ";")
      allRes$genes[i] <- paste(raw.data[[1]][p, "gene"], collapse = ";")
      allRes$names[i] <- paste(raw.data[[1]][p, "name"], collapse = ";")
    }

    results[[length(results) + 1]] <- list(GOdata = GOdata,
                                           resultFisher = resultFisher,
                                           table = allRes)
    names(results)[[length(results)]] <- group

    if(view) {
      View(allRes, paste(if(hasArg(name)) name, ontology, group, sep = "_"))
    }


  }





  if(save) {
    saveThis(results, name = name, destination = destination)
  }


  if(print) {

    if(!dir.exists("./GO")) {
      dir.create("./GO")
    }

    if(!hasArg(name)) {
      name <- paste(groups, collapse = "_")
    }


    if(dir.exists(paste0("./GO/", name))) {

      x <- 1

      while(dir.exists(paste0("./GO/", name, "_", x))) {
        x <- x + 1
      }

      path <- paste0("./GO/", name, "_", x)

    }

    else {

      path <- paste0("./GO/", name)

    }

    dir.create(path)

    setwd(path)

    for(i in 1:length(groups)) {

      printGraph(results[[i]][[1]],
                 results[[i]][[2]],
                 firstSigNodes = 20,
                 fn.prefix = paste(ontology, groups[i], sep = "_"),
                 useInfo = "all",
                 pdfSW = TRUE)

    }

    wd()

  }



}