setGenomicFeatures: Annotation of Hi-C contact map
In HiTC: High Throughput Chromosome Conformation Capture analysis

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

Annotate a Hi-C contact map with the genomic local features (i.e. GC content, mappability, effective fragment length)

1	setGenomicFeatures(x, cutSites, minFragMap=.5, effFragLen=1000)

`x`	`HTCexp` object to annotate
`cutSites`	`GRangesList` or `GRanges` object with restriction sites annotation obtained using the `getAnnotatedRestrictionSites` function
`minFragMap`	Minimum Fragment Mappbility. All fragments with a lower mappability are not used for the annotation.
`effFragLen`	Efective Fragment Length. Size of specific fragment ligation

The function require the restriction sites annotation as provided by the getAnnotatedRestrictionSites function. The restriction sites are first filtered according to their mappability. This threshold has to be defined according to the data pre-processing. All remaining restriction sites are then intersected with the genomic bins of the contact map. All restriction sites included within a bin are averaged. The effective fragment length is defined as the size of specific ligation product. (See Yaffe and Tanay, 2011). In this paper, the authors define specific ligation as sum of distance to cutter sites (d1+d2) <= 500 bp. Such criterion implies that d1<=500 bp and d2 <= 500 bp. So for each fragment end, only reads mapped within 500 bp to cutter sites are used for downstream analysis. All defults paramters correspond to the ones used in the HiCNorm method.

Returns a HTCexp object with local genomic features annotations.

N. Servant

normLGF, setGenomicFeatures

## Not run: 
require(BSgenome.Hsapiens.UCSC.hg18)
require(rtracklayer)

##Lieberman data
exDir <- system.file("extdata", package="HiTC")
l <- sapply(list.files(exDir, pattern=paste("HIC_gm06690_"), full.names=TRUE),
            import.my5C)
hiC <- HTClist(l)
hiC <- hiC[isIntraChrom(hiC)]
names(hiC)

## Mappability data From http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeMapability/
map_hg18<- import("wgEncodeCrgMapabilityAlign100mer.bw", format="BigWig")

## Get the genomic feature of the HiC chr12 data
cutSites <- getAnnotatedRestrictionSites(resSite="AAGCTT", overhangs5=1, chromosomes=seqlevels(hiC), genomePack="BSgenome.Hsapiens.UCSC.hg18", wingc=200, mappability=map_hg18, winmap=500)

chr12_annot <- setGenomicFeatures(hiC$chr12chr12, cutSites)

## End(Not run)