distFitMonotone: Fit the distance dependency
In FourCSeq: Package analyse 4C sequencing data

Description Usage Arguments Value Author(s)

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.

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

`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.