smoothMonotoneUMI4C: Monotone smoothing of the DDS object VST counts

In Pasquali-lab/UMI4Cats: UMI4Cats: Processing, analysis and visualization of UMI-4C chromatin contact data

Monotone smoothing of the DDS object VST counts

Description

Takes the variance stabilized count values and calculates a symmetric monotone fit for the distance dependency. The signal trend is fitted using the fda package. The position information about the viewpoint have to be stored in the metadata as metadata(dds)[['bait']].

Usage

smoothMonotoneUMI4C(dds, alpha = 20, penalty = 0.1)

Arguments

dds	DDS object as generated by vstUMI4C with the variance stabilized count values.
alpha	Approximate number of fragments desired for every basis function of the B-spline basis. floor((max(number of fragments)) / alpha) is passed to create.bspline.basis as nbasis argument. 4 is the minimum allowed value. Default: 20.
penalty	Amount of smoothing to be applied to the estimated functional parameter. Default: 0.1.

Details

This function computes the smoothing function for the VST values, based on fda package, and calculates a symmetric monotone fit counts for the distance dependency

Value

DDS object with monotone smoothed fit counts.

Pasquali-lab/UMI4Cats documentation built on Nov. 3, 2024, 3:10 p.m.