createRandomRegions {regioneR} | R Documentation

## Create Random Regions

### Description

Creates a set of random regions with a given mean size and standard deviation.

### Usage

    createRandomRegions(nregions=100, length.mean=250, length.sd=20, genome="hg19", mask=NULL, non.overlapping=TRUE)

### Arguments

`nregions` | The number of regions to be created.
`length.mean` | The mean size of the regions created. This is not guaranteed to be the mean of the final region set. See note.
`length.sd` | The standard deviation of the region size. This is not guaranteed to be the standard deviation of the final region set. See note.
`genome` | The reference genome to use. A valid genome object. Either a `GenomicRanges` or `data.frame` containing one region per whole chromosome or a character uniquely identifying a genome in `BSgenome` (e.g. "hg19", "mm10" but not "hg"). Internally it uses `getGenomeAndMask`.
`mask` | The set of regions specifying where a random region can not be (centromeres, repetitive regions, unmappable regions...). A region set in any of the accepted formats (`GenomicRanges`, `data.frame`, ...). `NULL` will try to derive a mask from the genome (currently only works is the genome is a character string) and `NA` explicitly gives an empty mask.
`non.overlapping` | A boolean stating whether the random regions can overlap (FALSE) or not (TRUE).

### Details

A set of nregions will be created and randomly placed over the genome. The lengths of the region set will follow a normal distribution with a mean size `length.mean` and a standard deviation `length.sd`. The new regions can be made explicitly non overlapping by setting `non.overlapping` to TRUE. A mask can be provided so no regions fall in a forbidden part of the genome.

### Value

It returns a `GenomicRanges` object with the regions resulting from the randomization process.

### Note

If the standard deviation of the length is large with respect to the mean, negative lengths might be created. These region lengths will be transfromed to into a 1 and so the, for large standard deviations the mean and sd of the lengths are not guaranteed to be the ones in the parameters.

### See Also

`getGenome`, `getMask`, `getGenomeAndMask`, `characterToBSGenome`, `maskFromBSGenome`, `randomizeRegions`, `resampleRegions`

### Examples

    genome <- data.frame(c("chr1", "chr2"), c(1, 1), c(180000000, 20000000))
    mask <- data.frame("chr1", c(20000000, 100000000), c(22000000, 130000000))

    createRandomRegions(nregions=10, length.mean=1000, length.sd=500)

    createRandomRegions(nregions=10, genome=genome, mask=mask, non.overlapping=TRUE)

[Package regioneR version 1.16.5 Index]