MareyMap (version 1.3.1)

MMSpline3-class: Class "MMSpline3" Interpolation using cubic splines

Description

MMSPline3 is a S4 class providing an interpolation method for MareyMap. Interpolation is done using cubic splines. The class uses smooth.spline to carry out the interpolation.

Objects from the Class

Objects can be created by calls of the form new("MMSpline3", ...). However you may instead use the function MMSpline3() and adjust the parameters afterwards using the accessor functions.

Slots

type:

Object of class "character" indicate which type of smoothing is applied, applicable values are "cross-validation", "spar" and "degree of freedom"

gcv:

Object of class "logical" indicating whether generalized cross validation is to be used when smoothing via cross validation.

df:

Object of class "numeric" holding the degree of freedom to use when the smoothing is done using degree of freedom

spar:

Object of class "numeric" value of the "spar" to be taken when smoothing the "spar" method.

model:

Object of class "ANY" slot used to keep the smooth.spline object after the interpolation.

name:

Object of class "character" holding the name of the interpolation.

color:

Object of class "character" holding the color of the interpolation

physicalPositions:

Object of class "vector" holding the valid physical positions of the map on which the interpolation is applied.

rates:

Object of class "vector" holding the local recombination rates at the position of each marker.

visible:

Object of class "logical" indicating whether the interpolation is to be drawn or not.

persistent:

Object of class "logical" indicating whether or not the interpolation should be taken into account when saving to text file.

Extends

Class "Interpolation", directly.

Methods

df<-

signature(object = "MMSpline3", value = "numeric"): Changes the value of the degree of freedom.

df

signature(object = "MMSpline3"): returns the value of the degree of freedom.

gcv<-

signature(object = "MMSpline3", value = "logical"): Turns on or off the generalized cross validation.

gcv

signature(object = "MMSpline3"): indicates whether the generalized cross validation is on or not.

createOrder

signature(object = "MMSpline3"): see Interpolation-class

interpolate

signature(object = "MMSpline3", map = "MareyMap"): carries out the interpolation on the map passed as parameter. Called automatically when an interpolation is added to a map

plotModel

signature(object = "MMSpline3"): Plot the interpolation's model of the Marey curve.

plotRate

signature(object = "MMSpline3"): Plots the variations of the recombination rates across a mapomosome.

query

signature(object = "MMSpline3", pos = "numeric"): query the estimation of the recombination rate in a specific position (or a vector of specific positions)

spar<-

signature(object = "MMSpline3", value = "numeric"): Changes the value of the spar.

spar

signature(object = "MMSpline3"): returns the value of the spar.

type<-

signature(object = "MMSpline3", value = "character"): Changes the type of smoothing to be used.

type

signature(object = "MMSpline3"): returns the smoothing method used.

userParam

signature(object = "MMSpline3"): returns informations about the user parameter, used by tcl/tk interface but not that useful for a command line user.

See Also

smooth.spline Interpolation-class MareyMap-class

Examples

data(Homo_sapiens_mean)
human7 <- Homo_sapiens_mean[["Chromosome 07"]]
itr1 <- MMSpline3()
color(itr1) <- "red"
spar(itr1) <- 0.05
human7 <- human7 + itr1
plot(human7)