normLGF {HiTC} | R Documentation

## Local Genomic Feature (LGF) normalization

### Description

Parametric model to remove systematic biases in the raw contact maps

### Usage

    normLGF(x, family=c("poisson", "nb"))

### Arguments

`x` | object that inherits from class `HTCexp`
`family` | parametric model to fit (poisson or nb)

### Details

This function implements the HiCNorm method proposed by Hu et al. Briefly, the method uses a generalized linear model to correct the systematic biases (effective fragment length, GC content, mappability) in a Hi-C contact map.

### Value

Returns a `HTCexp` object with a normalized contact map.

### Author(s)

N. Servant, M. Hu, S. Selvaraj

### References

Hu M, Deng K, Selvaraj S, Qin Z, Ren B, Liu JS. HiCNorm: removing biases in Hi-C data via Poisson regression. Bioinformatics. 2012;28(23):3131-3.

### See Also

`getAnnotatedRestrictionSites`, `setGenomicFeatures`

### Examples

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

    ##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 chromosome 12
    hiC_annot <- HTClist(lapply(hiC, setGenomicFeatures, resSite="AAGCTT", overhangs5=1, genomePack="BSgenome.Hsapiens.UCSC.hg18", wingc=200, mappability=map_hg18, winmap=500))
    hiC_annot$chr12chr12

    ## Normalize the data
    hiCnorm <- HTClist(lapply(hiC_annot, normLGF))

    ## End(Not run)

[Package HiTC version 1.32.0 Index]