Calculates the distribution of overlaps for a query set to a reference assembly

Source: R/partition-plots.R

This function is a wrapper for calcPartitions and calcPartitionPercents that uses built-in partitions for a given reference genome assembly.

calcPartitionsRef(query, refAssembly, bpProportion = FALSE)

Arguments

query

A GenomicRanges or GenomicRangesList object with query regions

refAssembly

A character vector specifying the reference genome assembly (*e.g.* 'hg19'). This will be used to grab annotation models with getGeneModels

bpProportion

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.

Value

A data.frame indicating the number of query region overlaps in several genomic partitions.

Examples

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