This function is a wrapper for
calcPartitionPercents that uses built-in
partitions for a given reference genome assembly.
calcPartitionsRef(query, refAssembly, bpProportion = FALSE)
A GenomicRanges or GenomicRangesList object with query regions
A character vector specifying the reference genome
assembly (*e.g.* 'hg19'). This will be used to grab annotation
logical indicating if overlaps should be calculated based on number of base pairs overlapping with each partition. bpProportion=FALSE does overlaps in priority order, bpProportion=TRUE counts number of overlapping base pairs between query and each partition.
A data.frame indicating the number of query region overlaps in several genomic partitions.
calcPartitionsRef(vistaEnhancers, "hg19") #> Calculating overlaps... #> partition Freq #> 1 exon 30 #> 2 fiveUTR 11 #> 3 intergenic 828 #> 4 intron 441 #> 5 promoterCore 5 #> 6 promoterProx 12 #> 7 threeUTR 12