getAnnotatedRestrictionSites: Annotation of restriction sites

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

View source: R/normalize_hiC.R

Description

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

Usage

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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

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## 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)

bioinfo-pf-curie/HiTC documentation built on May 17, 2019, 6:39 p.m.