dozmorovlab/HiCdiff
HiCdiff: Joint normalization and comparative analysis of multiple Hi-C datasets

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SCN: SCN normalization from Cournac 2012

SCN: SCN normalization from Cournac 2012
In dozmorovlab/HiCdiff: HiCdiff: Joint normalization and comparative analysis of multiple Hi-C datasets

Description Usage Arguments Details Value Examples

View source: R/Cournac_normalization.R

Description

SCN normalization from Cournac 2012

Usage

1
SCN(a, max.iter = 5)

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

1
2
m <- matrix(rpois(100, 5), 10, 10)
SCN(m)

dozmorovlab/HiCdiff documentation built on May 20, 2019, 11:13 a.m.

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