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

Specifies calling of narrow and/or broad marks.

narrow

Writes UCSC narrowPeak calls.

broad

Writes UCSC gappedPeak calls.

both

Writes narrow and broad calls.

narrow 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.minMeanSignal

Keeps regions whose covered-BP-weighted mean signal reaches the supplied descriptive threshold. Disable with null.

matchingParams.mergeToleranceBP

Sets the maximum gap eligible for broad-family merging. A positive value is required for broad and combined modes.

matchingParams.maxRegionBP

Sets the maximum outer width for a broad family. A positive value is required for broad and combined modes.

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.

observationParams.precisionMultiplierMin and observationParams.precisionMultiplierMax

Bound observation precision multipliers. The defaults are 0.1 and 10.0.

processParams.precisionMultiplierMin and processParams.precisionMultiplierMax

Bound process precision multipliers. The defaults are 1.0e-4 and 10.0. Because \(Q_i=Q_0/\kappa_i\), the multipliers let the local frequency response adapt: smaller \(\kappa_i\) admits faster variation, whereas larger \(\kappa_i\) favors smoother variation.

outputParams.stateShrinkageEnabled

Enables experimental posterior state shrinkage and defaults to True. Set it to False to disable it. Use the shrunk state as a visualization or ranking track, rather than as a replacement for the fitted state.