distFitMonotone {FourCSeq} | R Documentation

## Fit the distance dependency

### Description

`distFitMonotone` takes the variance stabilized count values and calculates a monotone fit for the distance dependency. The position information about the viewpoint is stored in `fragData`. The signal trend is fitted for the data left and right to the viewpoint separately using the fda package.

### Usage

    distFitMonotone(count, fragData, alpha = 20, penalty = 0.1,
      removeZeros = FALSE, ...)

### Arguments

`count` | Matrix of variance stabilized count data in the defined interval around the viewpoint.
`fragData` | Data frame with all the information on restriction fragments and the interval around the viewpoint.
`alpha` | Approximate number of fragments between two breaks of the B-spline basis. `floor((number of fragments))/alpha)` is passed to `create.bspline.basis` as `nbasis` argument (if this value is smaller than 4, 4 is the default value for `nbasis`). Default is `20`.
`penalty` | Penalty term passed to `fdPar` as `lambda` argument. Default is `0.1`.
`removeZeros` | Defines if zero values should be removed from the fit. Default is `FALSE`.
`...` | Additional parameters.

### Value

Returns a matrix with z-score values of all fragments around the given viewpoint.

### Author(s)

Felix A. Klein, felix.klein@embl.de

[Package FourCSeq version 1.16.0 Index]