R/Genesets-enrichr.R

In MIGSA: Massive and Integrative Gene Set Analysis

#' List and download gene sets from enrichr database
#'
#' \code{enrichrGeneSets} lists the database names present at enrichr.
#' \code{downloadEnrichrGeneSets} creates a list of GeneSetCollection
#' objects downloading the specified ones from enrichr website
#' (https://amp.pharm.mssm.edu/Enrichr/).
#'
#' @param pattern character indicating a pattern to filter the database names.
#' @param geneSetNames list of characters with the names of the gene sets to
#' download. Must be listed at \code{\link{enrichrGeneSets}}.
#' @param deleteMultipleEntrez logical indicating if multiple Entrez IDs should
#' be deleted or repeated.
#' Note: Enrichr uses Gene Symbol, if org.Hs.eg translates it into several
#' Entrez IDs then if deleteMultipleEntrez == FALSE all Entrez are removed else
#' all are included.
#' @param ... not in use.
#'
#' @return enrichrGeneSets: character with present database names.
#' downloadEnrichrGeneSets: list of GeneSetCollection objects (Genes are with
#' their EntrezGene ID).
#'
#' @docType methods
#' @name Genesets-enrichr
#' @rdname Genesets-enrichr
#' @seealso \code{\link{as.Genesets}}
#' @seealso \code{\link{geneSetsFromFile}}
#' @seealso \code{\link{loadGo}}
#'
#' @examples
#' ## Lets list all the gene sets that can be downloaded from Enichr website.
#' enrichrGeneSets()
#' \dontrun{
#' ## Now lets list only the gene sets that have BioCarta in their names
#' ## (different BioCarta versions).
#' enrichrGeneSets("BioCarta")
#'
#' ## And lets download the latest BioCarta gene sets from Enrichr.
#' ## Make sure you use the same names as listed with enrichrGeneSets() .
#' biocartaGSs <- downloadEnrichrGeneSets(c("BioCarta_2015"))
#' }
setGeneric(name = "Genesets-enrichr", def = function(pattern) {
  standardGeneric("Genesets-enrichr")
})

#' @name enrichrGeneSets
#' @rdname Genesets-enrichr
#' @aliases enrichrGeneSets,character-method
#' @exportMethod enrichrGeneSets
#'
setGeneric(name = "enrichrGeneSets", def = function(pattern = ".*") {
  standardGeneric("enrichrGeneSets")
})

#' @rdname Genesets-enrichr
#' @aliases enrichrGeneSets,character-method
#'
#' @importFrom Biobase testBioCConnection
#' @importFrom jsonlite fromJSON
#'
setMethod(
  f = "enrichrGeneSets",
  signature = character(),
  definition = function(pattern = ".*") {
    if (!testBioCConnection()) stop("You must have internet connection.")

    # enrichr url
    datasetStatisticsUrl <-
      "https://amp.pharm.mssm.edu/Enrichr/datasetStatistics"

    # donwload genesets list (basic info)
    datasetStatistics <- try({
      t(do.call(
        rbind,
        fromJSON(datasetStatisticsUrl)$statistics
      ))
    })
    if (inherits(datasetStatistics, "try-error")) {
      return(NA)
    }

    datasetStatistics <- apply(datasetStatistics, 2, unlist)
    datasetStatistics <- data.frame(datasetStatistics)

    # giving some format
    datasetStatistics[, c(1, 2, 5)] <-
      apply(datasetStatistics[, c(1, 2, 5)], 2, as.numeric)
    datasetStatistics[, 3:4] <-
      apply(datasetStatistics[, 3:4], 2, as.character)

    # filtering with pattern (by default returns all)
    datasetStatistics <- datasetStatistics[
      grep(pattern, datasetStatistics$libraryName, ignore.case = !FALSE),
    ]

    # order by gene set name
    datasetStatistics <-
      datasetStatistics[order(datasetStatistics$libraryName), ]

    return(datasetStatistics)
  }
)

#' @name downloadEnrichrGeneSets
#' @rdname Genesets-enrichr
#' @aliases downloadEnrichrGeneSets,character-method
#' @exportMethod downloadEnrichrGeneSets
#'
setGeneric(name = "downloadEnrichrGeneSets", def = function(geneSetNames, ...) {
  standardGeneric("downloadEnrichrGeneSets")
})

#' @rdname Genesets-enrichr
#' @aliases downloadEnrichrGeneSets,ANY-method
#'
#' @importFrom AnnotationDbi as.list
#' @importFrom Biobase testBioCConnection
#' @importFrom futile.logger flog.info
#' @importFrom GSEABase GeneSet GeneSetCollection GOCollection NullCollection
#' @importFrom org.Hs.eg.db org.Hs.egALIAS2EG
#'
setMethod(
  f = "downloadEnrichrGeneSets",
  signature = c("character"),
  definition = function(geneSetNames,
                        deleteMultipleEntrez = !FALSE) {
    # enrichr url
    downloadUrlFst <-
      "https://amp.pharm.mssm.edu/Enrichr/geneSetLibrary?mode=text&libraryName="

    # filtering invalid gene sets
    if (length(geneSetNames) < 1) {
      stop("No gene sets found to download from Enrichr")
    }

    if (!testBioCConnection()) stop("You must have internet connection.")

    # to translate Symbols to Entrez
    symbol2entrez <- as.list(org.Hs.egALIAS2EG)

    libraries <- lapply(geneSetNames, function(libName) {
      # if name starts with GO then is_GO true
      is_GO <- grepl("^GO_", libName)
      collection <- NullCollection()
      if (is_GO) {
        collection <- GOCollection()
      }

      actUrl <- paste(downloadUrlFst, libName, sep = "")
      # downloading gene set
      tmp <- try({
        readLines(actUrl)
      })
      if (inherits(tmp, "try-error")) {
        return(NA)
      }

      flog.info(paste("Downloaded", libName))
      tmp <- strsplit(tmp, "\t")
      flog.info("Converting Symbol to Entrez")
      geneSets <- lapply(tmp, function(actGS) {
        actId <- actGS[[1]]
        actName <- actGS[[2]]
        entrez <- lapply(actGS[2:length(actGS)], function(symbol) {
          # trying to convert from Symbol to Entrez
          translates <- symbol2entrez[[symbol]]

          if (is.null(translates)) {
            # some times Enrichr returns gene symbols followed by a
            # ',1.0' , this is some kind of fixing it.
            translates <- symbol2entrez[[gsub(",1.0", "", symbol)]]
          }

          # if multiple Entrez returned then delete them or not
          if (length(translates) > 1 && deleteMultipleEntrez) {
            translates <- NULL
          }

          return(translates)
        })
        entrez <- Reduce(union, entrez)

        res <- NA

        # if returned any gene, then create the Geneset
        if (length(entrez) > 0) {
          res <- GeneSet(entrez,
            setIdentifier = actName,
            setName = actId, geneIdType = EntrezIdentifier(),
            collectionType = collection
          )
        }

        return(res)
      })

      # filter invalid gene sets
      geneSets <- geneSets[!is.na(geneSets)]
      res <- NA

      if (length(geneSets) > 0) {
        res <- GeneSetCollection(geneSets)
      }

      return(res)
    })
    names(libraries) <- geneSetNames
    libraries <- libraries[!is.na(libraries)]

    return(libraries)
  }
)