Class "MMSlidingWindow" Interpolation method plug-in for MareyMap

Description

This package provides an interpolation method that estimates the recombination rates using a sliding window approach.

Objects from the Class

Objects can be created by calls of the form new("MMSlidingWindow", ...) or using the method SlidingWindow().

Slots

size:

Object of class "integer", the size of the windows in base pairs

shift:

Object of class "integer", the distance in number of base pairs between the centers of two consecutive windows.

threshold:

Object of class "integer" minimum number of markers in a window to perform the regression

results:

Object of class "vector" position of the model curve estimated at the center f each window.

name:

Object of class "character" see Interpolation-class

color:

Object of class "character" see Interpolation-class

physicalPositions:

Object of class "vector" see Interpolation-class

rates:

Object of class "vector" see Interpolation-class

visible:

Object of class "logical" see Interpolation-class

persistent:

Object of class "logical" see Interpolation-class

Extends

Class "Interpolation", directly.

Methods

createOrder

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

interpolate

signature(object = "MMSlidingWindow", map = "MareyMap"): see Interpolation-class

plotModel

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

plotRate

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

query

signature(object = "MMSlidingWindow", pos = "numeric"): see Interpolation-class

shift<-

signature(object = "MMSlidingWindow"): updates the value of the parameter shift

shift

signature(object = "MMSlidingWindow"): returns the value of the parameter shift

size<-

signature(object = "MMSlidingWindow"): updates the value of the parameter size

size

signature(object = "MMSlidingWindow"): returns the value of the parameter size

threshold<-

signature(object = "MMSlidingWindow"): updates the value of the parameter threshold

threshold

signature(object = "MMSlidingWindow"): returns the value of the parameter threshold

userParam

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

Author(s)

Clement Rezvoy <rezvoy@biomserv.univ-lyon1.fr>

References

~put references to the literature/web site here ~

See Also

Interpolation-class

Examples

data(mareymaps)
human7 <- mareymaps[["Homo sapiens (deCODE)","Chromosome 07"]]
library(MMSlidingWindow)
itr1 <- MMSlidingWindow()
color(itr1) <- "red"
size(itr1) <- 5000000
shift(itr1) <- 1000000
human7 <- human7 + itr1
plot(human7)