smoothMonotoneUMI4C {UMI4Cats} | R Documentation

## 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.

[Package UMI4Cats version 1.0.1 Index]