Normalizes biological biases such as GC content and repeated regions. Uses the Knight-Ruiz balancing algorithm to transform interaction matrices into doubly stochastic matrices, with sum of each row and sum of each column equal to 1.

normalizeBiologicalBiases(object)

Arguments

object

A HiCDOCDataSet.

Value

A HiCDOCDataSet with normalized interactions.

See also

Examples

data(exampleHiCDOCDataSet) object <- exampleHiCDOCDataSet object <- filterSparseReplicates(object)
#> Keeping replicates filled with at least 30% non-zero interactions.
#> Removed interactions matrix of chromosome W, condition 2, replicate R1 filled at 0%.
#> Removed interactions matrix of chromosome X, condition 1, replicate R2 filled at 2.347%. #> Removed interactions matrix of chromosome X, condition 2, replicate R1 filled at 0%.
#> Removed interactions matrix of chromosome Z, condition 1, replicate R1 filled at 0%. #> Removed interactions matrix of chromosome Z, condition 2, replicate R1 filled at 0%. #> Removed interactions matrix of chromosome Z, condition 2, replicate R2 filled at 0%. #> Removed interactions matrix of chromosome Z, condition 3, replicate R1 filled at 0%. #> Removed interactions matrix of chromosome Z, condition 3, replicate R2 filled at 0%.
#> Removed 8 replicates in total.
object <- filterWeakPositions(object)
#> Keeping positions with interactions average greater or equal to 1.
#> Chromosome W: 0 positions removed, 80 positions remaining.
#> Chromosome X: 2 positions removed, 118 positions remaining.
#> Chromosome Y: 3 positions removed, 157 positions remaining.
#> Chromosome Z: 0 positions removed, 200 positions remaining.
#> Removed 5 positions in total.
object <- normalizeBiologicalBiases(object)
#> Chromosome W: normalizing biological biases.
#> Chromosome X: normalizing biological biases.
#> Chromosome Y: normalizing biological biases.
#> Chromosome Z: normalizing biological biases.