Parameter Guidance

Most parameters can be left at their default values. The following sections provide guidance on key arguments that may be useful to adjust for specific applications.

Peak Calling Controls

matchingParams.peakMode

Selects ROCCO export shape.

narrow

Writes UCSC narrowPeak calls.

broad

Writes UCSC gappedPeak calls.

both

Writes narrow and broad calls. This is the default.

matchingParams.thresholdZ

Sets a one-sided \(z\)-score cutoff used to define the budget (max. proportion of genome called). Larger values will yield a smaller budget and fewer calls. Smaller values will yield a larger budget and more calls. The default value is 2.0.

matchingParams.minPeakScore

Filter selected peaks to those with an average signal above this threshold.

Uncertainty Score

matchingParams.uncertaintyScoreMode

state uses the fitted state track directly. lower_confidence uses state - matchingParams.uncertaintyScoreZ * uncertainty to penalize regions where estimates are uncertain.

matchingParams.uncertaintyScoreZ

Sets the multiplier used by lower_confidence scoring. Larger values penalize uncertain regions more strongly.

Estimation Controls

countingParams.intervalSizeBP

Sets the genomic bin size in base pairs. The default is 50 and is appropriate for most cases. Higher-resolution results may be obtained using 25, 10, etc. For detecting domain-level enriched-regions in broad marks like H3K27me3, larger values (100, 250, etc.) should suffice.

fitParams.ECM_backgroundLengthScaleMultiplier

Sets the multiplier that converts the inferred correlation-length into the soft background fitting window. Larger values softly restrict the shared background estimate \(g_{[i=1,\ldots,i=n]}\) to lower frequencies.

outputParams.stateShrinkageSpikeOddsMultiplier

(Experimental) Ignored if posterior state shrinkage is disabled entirely (outputParams.stateShrinkageEnabled). Values above 1.0 multiply fitted point-null odds upward, which can reduce false positives in low-signal regions. Values below 1.0 multiply those odds downward.