MareyMap-class {MareyMap}

Class "MareyMap"

Description

The class holds the physical and genetic positions of a marey map

Objects from the Class

Objects can be created by calls of the form new("MareyMap", ...) or using the function MareyMap(). However, most of the time you can more conveniently use already constructed objects contained in (c.f. code examples)

Slots

setName:

Object of class "character"

mapName:

Object of class "character" containing the name of the map, usually the name of the mapomosome it is mapping.

markerNames:

Object of class "vector" containing the names of the markers of the map.

physicalPositions:

Object of class "vector" containing the physical positions of the markers.

geneticDistances:

Object of class "vector" containing the positions of the markers on the genetic map.

markerValidity:

Object of class "vector" indicating for each marker if it is to be taken into account for interpolations.

interpolations:

Object of class "list" containing the interpolations calculated on the map.

Methods

[

signature(x = "MareyMap"): returns a vector combining marker name, physical position, genetic distance and marker validity for the i th marker

[[<-

signature(x = "MareyMap"): replaces marker name, physical position, genetic distance and marker validity for the i th marker. value must be a vector containing 4 column named "name", "phys", "gen" and "valid".

[[<-

signature(x = "MareyMap", i = "ANY", j = "ANY", value = "ANY"): replaces marker name, physical position, genetic distance and marker validity for the i th marker. value must be a vector containing 4 column named "name", "phys", "gen" and "valid".

[[

signature(x = "MareyMap"): returns a vector combining marker name, physical position, genetic distance and marker validity for the i th marker

+

signature(e1 = "MareyMap", e2 = "Interpolation"): adds an interpolation to the map

coerce

signature(from = "MareyMap", to = "data.frame"): convert the Marey map into a data.frame.

coerce

signature(from = "MareyMap", to = "NULL"): returns NULL

coerce

signature(from = "data.frame", to = "MareyMap"): create a MareyMap from a data.frame.

geneticDistances<-

signature(object = "MareyMap"): replace the genetic distance with a new vector.

geneticDistances

signature(object = "MareyMap"): returns the genetic distances of the markers

interpolation<-

signature(object = "MareyMap", inter_name = "character", value = "Interpolation"): replaces the interpolation which name matches inter_name with the content of the parameter value.

interpolation

signature(object = "MareyMap", inter_name = "character"): returns the interpolation which name matches inter_name.

interpolations<-

signature(object = "MareyMap"): replace the list of interpolation with a new list.

interpolations

signature(object = "MareyMap"): returns the list of interpolations.

mapName<-

signature(object = "MareyMap"): replaces the name of the map

mapName

signature(object = "MareyMap"): returns the name of the map

markerNames<-

signature(object = "MareyMap"): replaces the marker names with a new vector of names

markerNames

signature(object = "MareyMap"): returns a vector containing the names of the markers

markerValidity<-

signature(object = "MareyMap"): replaces the marker validity with a new vector

markerValidity

signature(object = "MareyMap"): returns a vector containing information about the validity of the markers

physicalPositions<-

signature(object = "MareyMap"): replaces the vector of physical positions with a new vector

physicalPositions

signature(object = "MareyMap"): returns a vector containing the physical positions of the markers

plot

signature(x = "MareyMap", y = "missing"): plots the map as well as the interpolations (if any)

plotMarkers

signature(object = "MareyMap"): plots only the markers of the map, without plotting the interpolations

plotModels

signature(object = "MareyMap"): plot only the models of the interpolations

plotRates

signature(object = "MareyMap"): plots only the recombination rates

query

signature(object = "MareyMap", pos = "numeric"): returns the value of the local recombination rate at physical position pos as estimated by the interpolations defined on the map. Returns a list of integers (or NAs). each individual result may be accessed via result[[interpolation_name]]

removeMarker

signature(object = "MareyMap", value = "integer"): remove the marker number value.

setName<-

signature(object = "MareyMap", value = "ANY"): replaces the name of the set with a new character.

setName

signature(object = "MareyMap"): returns the name of the set.

validPositions

signature(object = "MareyMap"):

textFile

signature(object = "MareyMap", file = "character"): Writes the map to text file.

Warning

vectors markerNames, physicalPositions, geneticDistances and markerValidity must always retain the same length.

Author(s)

Aurélie Siberchicot [e-mail] and Clément Rezvoy

See Also

MapCollection-class MapSet-class

Examples

data(Homo_sapiens_male)
chr7 <- Homo_sapiens_male[["Chromosome 07"]]
chr7 <- chr7 + MMLoess()
par(mfrow = c(2, 1))
plotMarkers(chr7)