Performs KR (Knight-Ruiz) normalization on a Hi-C matrix

KRnorm(A)

Arguments

A	the matrix to be normalized - any columns/rows of 0's will be removed before being normalized.

Value

A KR normalized matrix

Details

Performs KR normalization. The function is a translation of the `Matlab` code provided in the 2012 manuscript. Knight PA, Ruiz D. A fast algorithm for matrix balancing. IMA Journal of Numerical Analysis. Oxford University Press; 2012; drs019.

Examples

m <- matrix(rpois(100, 5), 10, 10)
KRnorm(m)
#>           [,1]     [,2]     [,3]     [,4]     [,5]     [,6]     [,7]     [,8]
#>  [1,] 0.031717 0.159124 0.088584 0.018704 0.107713 0.091780 0.126376 0.076765
#>  [2,] 0.139233 0.074842 0.166658 0.070376 0.112580 0.092090 0.090574 0.077024
#>  [3,] 0.110731 0.027776 0.185557 0.104476 0.150417 0.076900 0.126057 0.021440
#>  [4,] 0.056111 0.093835 0.078357 0.132353 0.127035 0.108244 0.085170 0.090536
#>  [5,] 0.017952 0.090064 0.250694 0.105863 0.040644 0.103895 0.102184 0.069518
#>  [6,] 0.091780 0.069068 0.153800 0.086595 0.145452 0.148724 0.062690 0.017770
#>  [7,] 0.090269 0.090574 0.050423 0.127754 0.143058 0.062690 0.184973 0.069912
#>  [8,] 0.061412 0.038512 0.107199 0.162964 0.191175 0.106623 0.087390 0.074317
#>  [9,] 0.105620 0.088314 0.147494 0.062283 0.199270 0.040750 0.100199 0.119293
#> [10,] 0.123212 0.220766 0.147481 0.062278 0.079701 0.081493 0.080152 0.068161
#>           [,9]    [,10]
#>  [1,] 0.088017 0.211220
#>  [2,] 0.110393 0.066230
#>  [3,] 0.073747 0.122900
#>  [4,] 0.083045 0.145315
#>  [5,] 0.099635 0.119551
#>  [6,] 0.163001 0.061120
#>  [7,] 0.080159 0.100190
#>  [8,] 0.051126 0.119282
#>  [9,] 0.117239 0.019538
#> [10,] 0.039076 0.097681