SCN {HiCcompare} | R Documentation

## SCN normalization from Cournac 2012

### Description

SCN normalization from Cournac 2012

### Usage

    SCN(a, max.iter = 10)

### Arguments

`a` | The matrix to be normalized. Any cols/rows that sum to 0 will be removed before normalization.
`max.iter` | maximum number of iterations to be performed

### Details

Performs Sequential Component Normalization as described by Cournac. Coded using details in the manuscript. Cournac A, Marie-Nelly H, Marbouty M, Koszul R, Mozziconacci J. Normalization of a chromosomal contact map. BMC Genomics. 2012;13: 436. doi:10.1186/1471-2164-13-436

### Value

An SCN normalized matrix

### Examples

    m <- matrix(rpois(100, 5), 10, 10)
    SCN(m)

[Package HiCcompare version 1.9.0 Index]