Removes weak genomic positions whose interactions average is lower than the threshold.

filterWeakPositions(object, threshold = NULL)

Arguments

object

A HiCDOCDataSet.

threshold

The minimum average interaction for a position to be kept. If a position's average interaction with the entire chromosome is lower than this value in any of the replicates, it is removed from all replicates and conditions. Defaults to object$smallChromosomeThreshold which is originally set to defaultHiCDOCParameters$smallChromosomeThreshold = 1.

Value

A filtered HiCDOCDataSet.

Details

Detects weak genomic positions in each replicate, and removes them from all replicates to guarantee comparability across conditions when calling detectCompartments.

See also

Examples

data(exampleHiCDOCDataSet) object <- exampleHiCDOCDataSet object <- filterWeakPositions(object)
#> Keeping positions with interactions average greater or equal to 1.
#> Chromosome W: 0 positions removed, 80 positions remaining.
#> Chromosome X: 3 positions removed, 117 positions remaining.
#> Chromosome Y: 3 positions removed, 157 positions remaining.
#> Chromosome Z: 0 positions removed, 200 positions remaining.
#> Removed 6 positions in total.