getRestrictionFragmentsPerChromosome {HiTC} | R Documentation

## Get a list of DNA restriction fragments

### Description

Performs the detection of restriction sites on a given genome and convert this information as a list of restriction fragments.

### Usage

    getRestrictionFragmentsPerChromosome(resSite="AAGCTT", overhangs5=1,
    chromosomes=NULL, genomePack="BSgenome.Mmusculus.UCSC.mm9")

### Arguments

`resSite` | the sequence of the restriction site to look for. Default is HindIII restriction site
`overhangs5` | 5' overhangs on the DNA resulted from the cutting
`chromosomes` | vector of chromosome number to focus on. Default all the chromosomes for the specified genome.
`genomePack` | name of the genome package to access the DNA sequence

### Value

Returns a `GRanges` object with all restriction fragments for a given genome/chromosome.

### Author(s)

N. Servant

### See Also

`normLGF`, `setGenomicFeatures`, `getAnnotatedRestrictionSites`

### Examples

    ## Not run:
    ## Mappability data From http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeMapability/
    map_hg18<- import("wgEncodeCrgMapabilityAlign100mer.bw",format="BigWig")

    ## 1- Get the list of restriction fragments for Human hg18 after HindIII digestion
    resFrag <- getRestrictionFragmentsPerChromosome(resSite="AAGCTT", overhangs5=1, chromosomes="chrX", genomePack="BSgenome.Hsapiens.UCSC.hg18")

    ## End(Not run)

[Package HiTC version 1.38.0 Index]