getRestrictionFragmentsPerChromosome: Get a list of DNA restriction fragments

Description Usage Arguments Value Author(s) See Also Examples

View source: R/normalize_hiC.R

Description

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

Usage

1
2
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

1
2
3
4
5
6
7
8
## 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)

HiTC documentation built on Nov. 8, 2020, 8:27 p.m.