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
#> 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.