distFitMonotone: Fit the distance dependency

Description Usage Arguments Value Author(s)

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

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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


FourCSeq documentation built on Nov. 8, 2020, 7:08 p.m.