getRestrictionFragmentsPerChromosome: Get a list of DNA restriction fragments
In bioinfo-pf-curie/HiTC: High Throughput Chromosome Conformation Capture analysis

Description Usage Arguments Value Author(s) See Also Examples

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

1 2	getRestrictionFragmentsPerChromosome(resSite="AAGCTT", overhangs5=1, chromosomes=NULL, genomePack="BSgenome.Mmusculus.UCSC.mm9")

`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

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

N. Servant

normLGF, setGenomicFeatures, getAnnotatedRestrictionSites

## 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)