calcChromBins {GenomicDistributions} | R Documentation

## Calculates the distribution of a query set over the genome

### Description

Returns a data.table showing counts of regions from the query that overlap with each bin. In other words, where on which chromosomes are the ranges distributed? You must provide binned regions. Only the midpoint of each query region is used to test for overlap with the bin regions.

### Usage

    calcChromBins(query, bins)

### Arguments

`query` | A GenomicRanges or GenomicRangesList object with query regions
`bins` | Pre-computed bins (as a GRangesList object) to aggregate over; for example, these could be genome bins

### Value

A data.table showing where on which chromosomes ranges are distributed.

### Examples

    chromSizes = getChromSizes("hg19")
    genomeBins  = getGenomeBins(chromSizes)
    chromDistribution = calcChromBins(vistaEnhancers, genomeBins)

    vistaSftd = GenomicRanges::shift(vistaEnhancers, 100000)
    vistaSftd2 = GenomicRanges::shift(vistaEnhancers, 200000)
    calcChromBins(vistaEnhancers, GRangesList(vistaSftd, vistaSftd2))

[Package GenomicDistributions version 1.2.0 Index]