Removes chromosome replicates whose percentage of non-zero interactions is smaller than the threshold.

filterSparseReplicates(object, threshold = NULL)

Arguments

object

A HiCDOCDataSet.

threshold

The minimum percentage of non-zero interactions for a chromosome replicate to be kept. If a chromosome replicate's percentage of non-zero interactions is lower than this value, it is removed. Defaults to object$smallChromosomeThreshold which is originally set to defaultHiCDOCParameters$smallChromosomeThreshold = 30%.

Value

A filtered HiCDOCDataSet.

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.