SCN normalization from Cournac 2012

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

Value

An SCN normalized matrix

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

Examples

m <- matrix(rpois(100, 5), 10, 10)
SCN(m)
#>            [,1]       [,2]      [,3]      [,4]       [,5]      [,6]      [,7]
#>  [1,] 0.3303504 0.28315751 0.3303504 0.1415788 0.09438584 0.2831575 0.4719292
#>  [2,] 0.3478328 0.39752320 0.2484520 0.2981424 0.59628479 0.1490712 0.3478328
#>  [3,] 0.2457180 0.06142951 0.1842885 0.4300066 0.30714756 0.3685771 0.4914361
#>  [4,] 0.1513300 0.40354662 0.4035466 0.4035466 0.15132998 0.1513300 0.2522166
#>  [5,] 0.1787068 0.53612046 0.3574136 0.2233835 0.35741364 0.2233835 0.3127369
#>  [6,] 0.3464102 0.28867513 0.1732051 0.2886751 0.05773503 0.2309401 0.6928203
#>  [7,] 0.2867697 0.22941573 0.2294157 0.3441236 0.28676967 0.2867697 0.3441236
#>  [8,] 0.3841106 0.44812908 0.4481291 0.1920553 0.19205532 0.1920553 0.1920553
#>  [9,] 0.3289758 0.32897585 0.1315903 0.1315903 0.52636136 0.3289758 0.2631807
#> [10,] 0.2990252 0.25630730 0.1281536 0.3417431 0.29902518 0.3417431 0.2563073
#>            [,8]      [,9]     [,10]
#>  [1,] 0.3303504 0.2831575 0.4247363
#>  [2,] 0.1490712 0.0993808 0.1987616
#>  [3,] 0.0000000 0.4300066 0.2457180
#>  [4,] 0.4539899 0.1008867 0.4035466
#>  [5,] 0.1787068 0.3127369 0.3127369
#>  [6,] 0.3464102 0.1154701 0.1154701
#>  [7,] 0.3441236 0.2867697 0.4588315
#>  [8,] 0.2560738 0.1920553 0.4481291
#>  [9,] 0.2631807 0.3947710 0.2631807
#> [10,] 0.2563073 0.1281536 0.5980504