R/GeneOntologyFilter.R

In PriceLab/TReNA: Fit transcriptional regulatory networks using gene expression, priors, machine learning

#' @title Create a GeneOntologyFilter object
#'
#' @description
#' A GeneOntologyFilter object allows for filtering based on gene ontology (GO) terms. Its
#' associated \code{getCandidates} method uses an organism database and a GO term (e.g. GO:#######)
#' to filter a list of possible regulators factors to those that match the GO term.
#'
#' @include CandidateFilter.R
#' @import methods
#' @import org.Hs.eg.db
#'
#' @rdname GeneOntologyFilter-class
#' @aliases GeneOntologyFilter
#----------------------------------------------------------------------------------------------------
.GeneOntologyFilter <- setClass("GeneOntologyFilter",
                                contains="CandidateFilter",
                                slots=c(organismDatabase="OrgDb",
                                        GOTerm="character",
                                        quiet="logical"))
#----------------------------------------------------------------------------------------------------
printf <- function(...) print(noquote(sprintf(...)))
#----------------------------------------------------------------------------------------------------
# some candidate terms:
#  GO:0010467                        gene expression
#  GO:0097659   nucleic acid-templated transcription
#  GO:0001172           transcription, RNA-templated
#  GO:0006351           transcription, DNA-templated
#----------------------------------------------------------------------------------------------------
#' Create a CandidateFilter using Gene Ontology 
#'
#' @param organismDatabase An organism-specific database of type 'OrgDb'
#' @param GOTerm A character matching an accepted gene ontology term. The default term corresponds
#' to "transcription, DNA-templated". (default="GO:0006351")
#' @param quiet A logical denoting whether or not the filter should print output
#' 
#' @return A GeneOntologyFilter object
#'
#' @seealso  \code{\link{CandidateFilter}}
#'
#' @family CandidateFilter class objects
#'
#' @export
#'
#' @rdname GeneOntologyFilter-class
#' 
#' @examples
#' # Make a filter for "transcription, DNA-templated"
#' library(org.Hs.eg.db)
#' goFilter <- GeneOntologyFilter(org.Hs.eg.db, GOTerm="GO:0006351")

GeneOntologyFilter <- function(organismDatabase=org.Hs.eg.db::org.Hs.eg.db,
                               GOTerm="GO:0006351", quiet=TRUE)
{
    data.file <- system.file(package="trena", "extdata", "human.regulatory.genes.RData")
    load(data.file)
    .GeneOntologyFilter(organismDatabase=organismDatabase, GOTerm=GOTerm, quiet=quiet)
    
} # GeneOntologyFilter, the constructor
#----------------------------------------------------------------------------------------------------
#' Get candidate genes using a gene ontology filter
#'
#' @aliases getCandidates-GeneOntologyFilter
#'
#' @param obj An object of class GeneOntologyFilter
#'
#' @seealso \code{\link{GeneOntologyFilter}}
#'
#' @family getCandidate Methods
#'
#' @return A list, where one element a character vector of transcription factors that match
#' the GO term and the other is an empty data frame. 
#'
#' @export
#' 
#' @examples
#'
#' # Make a filter for "transcription, DNA-templated" and use it to filter candidates
#' library(org.Hs.eg.db)
#' goFilter <- GeneOntologyFilter(org.Hs.eg.db, GOTerm="GO:0006351")
#' candidates <- getCandidates(goFilter)

setMethod("getCandidates", "GeneOntologyFilter",

          function(obj){
              suppressMessages(
                  regulatory.genes <- AnnotationDbi::select(obj@organismDatabase, keys=obj@GOTerm,
                                                            keytype="GO", columns=c("SYMBOL", "GO"))$SYMBOL
              )
              list(tbl=data.frame(), tfs=regulatory.genes)
          }) # getCandidates
#----------------------------------------------------------------------------------------------------