R/aux_methods.R

In AUCell: AUCell: Analysis of 'gene set' activity in single-cell RNA-seq data (e.g. identify cells with specific gene signatures)

#' @title GeneSet methods
#' @description Functions to manipulate GeneSet and GeneSetCollection objects
#' (from package GSEABase)
#' @import GSEABase
#' @param geneSet One gene-set (\code{\link{GeneSet}})
#' @param geneSets Gene-set collection
#' (\code{\link{GeneSetCollection}})
#' @param geneNames Gene names (for subset)
#' @param newNames New names (to assign to the gene sets)
#' @return
#' - **nGenes()**: provides the number of genes in the gene-set,
#' or each of the gene-sets in a collection
#'
#' - **subsetGeneSets()**: Subsets each of the gene-sets in a collection
#' to contain only the genes inthe given list. Equivalent to intersect(),
#' but keeping the original gene-set name.
#'
#' - **setGeneSetNames()**: Modifies the name of each gene-set in a collection
#' @docType methods
#' @rdname GeneSet-methods
#'
#' @example inst/examples/example_geneSet_methods.R
#' @export
setGeneric("nGenes", signature="geneSet",
           function(geneSet)
           {
             standardGeneric("nGenes")
           })

#' @rdname GeneSet-methods
#' @aliases nGenes,GeneSet-method
setMethod("nGenes", "GeneSet",
  function(geneSet)
  {
    length(GSEABase::geneIds(geneSet))
  })

#' @rdname GeneSet-methods
#' @aliases nGenes,GeneSetCollection-method
setMethod("nGenes", "GeneSetCollection",
  function(geneSet)
  {
    setNames(sapply(geneSet, nGenes), names(geneSet))
  })

# equivalent to intersect, but keeping original name
#' @rdname GeneSet-methods
#' @export
setGeneric("subsetGeneSets",
  function(geneSets, geneNames)
  {
    standardGeneric("subsetGeneSets")
  })

#' @rdname GeneSet-methods
#' @aliases subsetGeneSets,GeneSetCollection-method
setMethod("subsetGeneSets", signature="GeneSetCollection",
  function(geneSets, geneNames)
  {
    GSEABase::GeneSetCollection(lapply(geneSets, function(x) {
      y <- x & geneNames
      GSEABase::setName(y) <- GSEABase::setName(x)
      y
    }))
  })

#' @rdname GeneSet-methods
#' @export
setGeneric("setGeneSetNames",
  function(geneSets, newNames)
  {
    standardGeneric("setGeneSetNames")
  })


#' @rdname GeneSet-methods
#' @aliases setGeneSetNames,GeneSetCollection-method
setMethod("setGeneSetNames", signature="GeneSetCollection",
  function(geneSets, newNames)
  {
    if(length(geneSets) != length(newNames))
      stop("The number of gene sets and new names do not match.")

    geneSets <- unlist(geneSets)
    for(i in seq_len(length(newNames)))
    {
      GSEABase::setName(geneSets[[i]]) <- newNames[i]
    }
    GSEABase::GeneSetCollection(geneSets)
  })