getAnnotatedRestrictionSites {HiTC} | R Documentation

## Annotation of restriction sites

### Description

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

### Usage

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

### 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
`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

### Details

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/.

### Value

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

### Author(s)

N. Servant

### See Also

`normLGF`, `setGenomicFeatures`

### Examples

    ## 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)

[Package HiTC version 1.38.0 Index]