R/FeatureTable.R

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

#' @title FeatureTable
#' @description A template for building documented, tested R6 classes
#' @name FeatureTable

#'
#' @examples
#'   rt <- FeatureTable()
#'
#' import R6
#' import data.table
#'
#' @export

FeatureTable = R6Class("FeatureTable",

    #--------------------------------------------------------------------------------
    private = list(tbl=NULL,
                   reference.genome=NULL,
                   target.gene=NULL
                   ),

    #--------------------------------------------------------------------------------
    public = list(
         #' @description
         #' Creates a new instance of this [R6][R6::R6Class] class.
         #' @param target.gene character, a recognized gene symbol
         #' @param reference.genome character, a recognized genome shorthand code, e.g., "hg38"
         #' @return a new instance o FeatureTable
        initialize = function(target.gene, reference.genome){
            private$target.gene <- target.gene
            private$reference.genome <- reference.genome
            private$tbl <- as.data.table(data.frame())
            },
        #------------------------------------------------------------
        #' @description accessor for the table
        #' @return the data.table
        getTable = function(){
            private$tbl
            },

        #------------------------------------------------------------
        #' @description establish the basic genomic regions, typically
        #'   transcription factor binding sites
        #' @param tbl.regions a data.frame with at least chrom, start end columns
        setFundamentalRegions = function(tbl.regions){
            stopifnot(all(c("chrom", "start", "end") %in% colnames(tbl.regions)))
            private$tbl <- as.data.table(tbl.regions)
            },

        #--------------------------------------------------------------------------
        #' @description annotate each of the intersecting fundamental regions with
        #'   the value of this feature
        #' @param tbl.feature a data.frame with chrom, start and end columns, and values
        #'        of interest described in the annotation guidel
        #' @param feature.genome character, a recognized genome shorthand code, e.g., "hg38"
        #' @param feature.guide a neme list identifying columns of interest in
        #'       tbl.bed, and the column names to use for them in the feature table
        #' @param default.values list matches feature.guide structure
        addRegionFeature = function(tbl.feature, feature.genome, feature.guide, default.values){
            stopifnot(all(c("chrom", "start", "end") %in% colnames(tbl.feature)))
            stopifnot(feature.genome == self$reference.genome)
                # first add default values to all rows
            for(feature in names(feature.guide)){
                source.feature.name <- feature.guide[[feature]]
                feature.class <- class(tbl.feature[[source.feature.name]])
                vec <- vector(feature.class, length=nrow(private$tbl))
                vec[seq_len(length(vec))] <- rep(default.values[[feature]], length(vec))
                private$tbl[[feature]] <- vec
               } # for feature
            if(nrow(tbl.feature) == 0) return()
            gr.ov <- findOverlaps(GRanges(tbl.feature), GRanges(private$tbl))
            if(length(gr.ov) == 0) return()
            tbl.ov <- as.data.frame(gr.ov)
            if(nrow(tbl.ov) == 0) return()
                # todo: eliminate redundant initialization to default value, 6th line below
            for(feature in names(feature.guide)){
                source.feature.name <- feature.guide[[feature]]
                feature.class <- class(tbl.feature[[source.feature.name]])
                vec <- vector(feature.class, length=nrow(private$tbl))
                vec[seq_len(length(vec))] <- rep(default.values[[feature]], length(vec))
                vec[tbl.ov$subjectHits] <- tbl.feature[[source.feature.name]][tbl.ov$queryHits]
                private$tbl[[feature]] <- vec
                } # for feature
            }, # addRegionFeature

        #------------------------------------------------------------------------
        #' @description annotate each of TFs, via their associated  motif mapped to
        #' the genome, with the value of the feature described in the feature guide
        #'
        #' @param tbl.feature a data.frame with gene and value columns, values
        #'        of interest described in the featureguide
        #' @param feature.name character use this string to name the new column
        #' @param default.value any the value to assign unmatched genes
        addGeneFeature = function(tbl.feature, feature.name, default.value){
            stopifnot(colnames(tbl.feature)[1] == "gene")
            stopifnot(ncol(tbl.feature) == 2)
            tbl.match <- as.data.frame(findMatches(tbl.feature$gene, private$tbl$tf))
            feature.class <- class(tbl.feature[,2])
            vec <- vector(feature.class, length=nrow(private$tbl))
            vec[seq_len(length(vec))] <- rep(default.value, length(vec))
            vec[tbl.match$subjectHits] <- tbl.feature[tbl.match$queryHits, 2]
            private$tbl[[feature.name]] <- vec
            }, # addGeneFeature

        #--------------------------------------------------------------------------
        #' @description annotate each region with a new column, the distance to TSS
        #'    upstream region starts will be negative, downstream will be positive
        #' @param tss.loc integer
        addDistanceToTSS = function(tss.loc){
            delta <- private$tbl$start - tss.loc
            private$tbl$distanceToTSS <- delta
            }

       ) # public

    ) # class
#--------------------------------------------------------------------------------