R/GenesetRes.R

In MIGSA: Massive and Integrative Gene Set Analysis

GenesetRes <- setClass(
  Class = "GenesetRes",
  slots = c(
    id = "character",
    name = "character",
    enriched = "logical",
    score = "numeric",
    pvalue = "numeric",
    genes = "character",
    enriching_genes = "character"
  ),
  prototype = list(
    score = as.numeric(NA),
    enriched = FALSE
  ),
  validity = function(object) {
    id_ok <- object@id != ""
    pvalue_ok <- (is.na(object@pvalue) ||
      (object@pvalue >= 0 && object@pvalue <= 1))
    genes_ok <- length(object@genes) > 0

    return(id_ok && pvalue_ok && genes_ok)
  }
)

setGeneric(name = "asCharacter", def = function(x, ...) {
  standardGeneric("asCharacter")
})

setMethod(
  f = "asCharacter",
  signature = c("GenesetRes"),
  definition = function(x, ...) {
    # translate a gene set result into a character vector
    actName <- ifelse(length(x@name) == 0, "", x@name)
    to <- c(x@id, actName, x@enriched, x@score, x@pvalue)
    to <- c(
      to, paste(x@enriching_genes, collapse = ", "),
      paste(x@genes, collapse = ", ")
    )

    # to avoid rare characters
    to <- iconv(to, to = "ASCII", sub = "")

    return(to)
  }
)

setGeneric(name = "id", def = function(object) {
  standardGeneric("id")
})

setMethod(f = "id", signature = "GenesetRes", definition = function(object) {
  return(object@id)
})

setGeneric(name = "id<-", def = function(object, value) {
  standardGeneric("id<-")
})

setReplaceMethod(
  f = "id", signature = "GenesetRes",
  definition = function(object, value) {
    object@id <- value
    validObject(object)
    return(object)
  }
)

setGeneric(name = "getName", def = function(object) {
  standardGeneric("getName")
})

setMethod(f = "getName", signature = "GenesetRes", definition = function(object) {
  return(object@name)
})

setGeneric(name = "getName<-", def = function(object, value) {
  standardGeneric("getName<-")
})

setReplaceMethod(
  f = "getName", signature = "GenesetRes",
  definition = function(object, value) {
    object@name <- value
    validObject(object)
    return(object)
  }
)