getRestrictionFragmentsPerChromosome {HiTC} | R Documentation |
Performs the detection of restriction sites on a given genome and convert this information as a list of restriction fragments.
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)