setGenomicFeatures {HiTC} | R Documentation

## Annotation of Hi-C contact map

### Description

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

### Usage

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

### Arguments

`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

### Details

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.

### Value

Returns a `HTCexp` object with local genomic features annotations.

### Author(s)

N. Servant

### See Also

`normLGF`, `setGenomicFeatures`

### Examples

    ## 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)

[Package HiTC version 1.24.0 Index]