R/Genesets-asGenesets.R

In MIGSA: Massive and Integrative Gene Set Analysis

#' Creates a GeneSetCollection from a list
#'
#' \code{as.Genesets} creates a GeneSetCollection object from the data present
#' in a list. Each element will parse to a GeneSet. For each list element, its
#' name will be the GeneSet setName, and the content are the genes.
#'
#' @param x list of character vectors which are the genes corresponding to each
#' GeneSet. The list must have names (unique).
#' @param is_GO logical indicating if this gene sets are from the Gene Ontology.
#' If true, then each GeneSet setName must be a GO id.
#' @param ... not in use.
#'
#' @return A GeneSetCollection object.
#'
#' @docType methods
#' @name as.Genesets
#' @rdname Genesets-as.Genesets
#' @seealso \code{\link{Genesets-enrichr}}
#' @seealso \code{\link{geneSetsFromFile}}
#' @seealso \code{\link{loadGo}}
#'
#' @exportMethod as.Genesets
setGeneric("as.Genesets", def = function(x, ...) {
  standardGeneric("as.Genesets")
})

#' @rdname Genesets-as.Genesets
#' @aliases as.Genesets,list-method
#'
#' @importFrom GSEABase GeneSet GeneSetCollection GOCollection NullCollection
#' @examples
#' ## Lets create a list with three manually created gene sets and load it as a
#' ## GeneSetCollection object.
#' myGs1 <- as.character(1:10)
#' myGs2 <- as.character(15:21)
#' myGs3 <- as.character(25:30)
#' myGssList <- list(myGs1, myGs2, myGs3)
#' names(myGssList) <- c("myGs1", "myGs2", "myGs3")
#' myGss <- as.Genesets(myGssList)
setMethod(
  f = "as.Genesets",
  signature = c("list"),
  definition = function(x, is_GO = FALSE) {
    if (length(unique(names(x))) != length(x)) {
      stop("The list must have all unique names.")
    }

    collection <- NullCollection()
    if (is_GO) {
      collection <- GOCollection()
    }

    act_gss <- lapply(names(x), function(act_id) {
      # these are the genes
      act_genes <- unique(x[[act_id]])

      # if there is any gene then create the Geneset
      if (length(act_genes) == 0 ||
        (length(act_genes) == 1 && act_genes == "")) {
        act_gs <- NULL
      } else {
        act_gs <- GeneSet(act_genes,
          setName = act_id,
          collectionType = collection, setIdentifier = ""
        )
      }
      return(act_gs)
    })
    # delete invalid genesets
    act_gss <- act_gss[!unlist(lapply(act_gss, is.null))]

    if (length(act_gss) < 1) {
      stop("Could not create any Geneset object,
                    maybe they where empty")
    }
    res <- GeneSetCollection(act_gss)
    return(res)
  }
)