getAnnotatedRestrictionSites: Annotation of restriction sites
In bioinfo-pf-curie/HiTC: High Throughput Chromosome Conformation Capture analysis

Description Usage Arguments Details Value Author(s) See Also Examples

Performs the annotation of all restriction sites of a given genome (i.e. GC content, mappability, effective fragment length)

1 2	getAnnotatedRestrictionSites(resSite="AAGCTT", overhangs5=1, chromosomes=NULL, genomePack="BSgenome.Mmusculus.UCSC.mm9", mappability=NULL, wingc=200, winmap=500)

`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
`wingc`	size of the window upstream and downstream the restriction site used to calculate the GC content
`mappability`	a `GRanges` with a 'score' describing the mappability of the genome
`winmap`	size of the window upstream and downstream the restriction site used to calculate the mappability

This function automatically annotate all the restriction sites of a given chromosome. The mappability is optional but strongly advice for Hi-C contact map normalization. This information can be easily download from public ressources like ftp://hgdownload.cse.ucsc.edu/gbdb/mm9/bbi/.

Returns a GRanges object annotation data upstream (U) and downstream (D) the restriction sites.

N. Servant

normLGF, setGenomicFeatures

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

## 1- Example of restriction sites annnotation
cutSites <- getAnnotatedRestrictionSites(resSite="AAGCTT", overhangs5=1, chromosomes="chr1", genomePack="BSgenome.Hsapiens.UCSC.hg18", wingc=200, mappability=map_hg18, winmap=500)

## End(Not run)