calcPartitionsRef {GenomicDistributions} | R Documentation

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

### Description

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

### Usage

    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")

[Package GenomicDistributions version 1.2.0 Index]