bnbc-package {bnbc} | R Documentation

## Bandwise normalization and batch correction of Hi-C data

### Description

Tools to normalize (several) Hi-C data from replicates.

### Details

The DESCRIPTION file:

Package: | bnbc
Version: | 1.12.0
Title: | Bandwise normalization and batch correction of Hi-C data
Description: | Tools to normalize (several) Hi-C data from replicates.
Authors@R: | c( person("Kipper", "Fletez-Brant", role = c("cre", "aut"), email = "cafletezbrant@gmail.com"), person(c("Kasper", "Daniel"), "Hansen", role = "aut"))
Depends: | R (>= 3.5.0), methods, BiocGenerics, SummarizedExperiment, GenomicRanges
Suggests: | BiocStyle, knitr, rmarkdown, RUnit
Imports: | Rcpp (>= 0.12.12), IRanges, rhdf5, data.table, GenomeInfoDb, S4Vectors, matrixStats, preprocessCore, sva, parallel, EBImage, utils
LinkingTo: | Rcpp
VignetteBuilder: | knitr
License: | Artistic-2.0
URL: | https://github.com/hansenlab/bnbc
BugReports: | https://github.com/hansenlab/bnbc/issues
biocViews: | HiC, Preprocessing, Normalization, Software
git_url: | https://git.bioconductor.org/packages/bnbc
git_branch: | RELEASE_3_12
git_last_commit: | 191bf12
git_last_commit_date: | 2020-10-27
Date/Publication: | 2020-10-27
Author: | Kipper Fletez-Brant [cre, aut], Kasper Daniel Hansen [aut]
Maintainer: | Kipper Fletez-Brant <cafletezbrant@gmail.com>

Index of help topics:

    ContactGroup-class      Class '"ContactGroup"'
    band                    Get Band
    bnbc                    Normalize Contact Matrices with BNBC
    bnbc-package            Bandwise normalization and batch correction of
                            Hi-C data
    boxSmoother             Smoothing Operations
    cgApply                 Apply-type methods
    cgEx                    Sample chr22 Data
    getBandIdx              Get Band Indices
    getBandMatrix           Get Band Matrix
    getGenomeIdx            Methods for manipulating cooler files
    getGroupZeros           Group Zero Operations

The package implements the bnbc method for normalizing Hi-C data across samples. The name is short for band-wise normalization and batch correction. The main workhorse is the `bnbc` function. We recommend using smoothing and library size normalization first.

The package implements the `ContactGroup` class for storing multiple Hi-C contact matrices. This is most naturally done with one object per chromosome, which is ugly.

We also have functions for applying over a `ContactGroup` (`cgApply`) and working with matrix bands `band, getBandIdx`.

### Author(s)

NA

Maintainer: NA

### References

Fletez-Brant et al. Distance-dependent between-sample normalization for Hi-C experiments. In preparation.

### See Also

`bnbc`, `ContactGroup`, `band`, `cgApply`.

### Examples

    data(cgEx)
    batches <- colData(cgEx)$Batch
    cgEx.cpm <- logCPM(cgEx)
    cgEx.smooth <- boxSmoother(cgEx, 5, mc.cores=1)
    cgEx.bnbc <- bnbc(cgEx.smooth, batches, 1e7, 4e4, bstart=2, nbands=4)

[Package bnbc version 1.12.0 Index]