Nearest Genes Function

DESCRIPTION

@@ -57,7 +57,7 @@ VignetteBuilder: knitr
 License: BSD_2_clause + file LICENSE
 biocViews: Software, GenomeAnnotation, GenomeAssembly, DataRepresentation, Sequencing, 
             Coverage, FunctionalGenomics, Visualization
-RoxygenNote: 7.1.1
+RoxygenNote: 7.1.2
 URL: http://code.databio.org/GenomicDistributions
 BugReports: http://github.com/databio/GenomicDistributions
 Encoding: UTF-8

NAMESPACE

@@ -15,6 +15,7 @@ export(calcFeatureDist)
 export(calcFeatureDistRefTSS)
 export(calcGCContent)
 export(calcGCContentRef)
+export(calcNearestGenes)
 export(calcNearestNeighbors)
 export(calcNeighborDist)
 export(calcOpenSignal)

R/nearest-genes.R

@@ -0,0 +1,34 @@
+#' Given a query and set of annotations, this function will calculate
+#' the nearest annotation to each region in the region set, as well
+#' as the nearest gene type and the distance to the nearest gene.
+#'
+#' @param query A GRanges or GRangesList object with query sets
+#' @param annotations A GRanges or GRangesList object with annotation sets
+#' 
+#' @return A data table that contains observations for each genomic region
+#'         and the associated aforementioned annotations.
+#' @export
+#' @examples
+#' queryFile = system.file("extdata", "vistaEnhancers.bed.gz", package="GenomicDistributions")
+#' query = rtracklayer::import(queryFile)
+#' data(TSS_hg19)
+#' 
+#' queryAnnotated = calcNearestGenes(query, TSS_hg19)
+calcNearestGenes =  function(query, annotation, gene_name_key="gene_id", gene_type_key="gene_biotype") {
+  .validateInputs(list(query=c("GRanges","GRangesList")))
+
+  # calculate the nearest annotations to given query
+  nearestIds = nearest(query, annotations)
+
+  # annotate neaest gene and type
+  query$nearest_gene = annotations[nearestIDs]$gene_id
+  query$nearest_gene_type = annotations[nearestIds]$gene_biotype
+
+  # annotate on the distance as well
+  query$nearest_distance = distance(query, annotations[nearestIds])
+
+  # dump a query to a data table and return
+  dt = grToDt(query)
+
+  return(dt)
+}