Help for package MareyMap

Title:

Estimation of Meiotic Recombination Rates Using Marey Maps

Version:

1.3.10

Depends:

R (≥ 2.10)

Imports:

graphics, grDevices, methods, stats, tcltk, tools, utils

Suggests:

tkrplot

License:

GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]

Description:

Local recombination rates are graphically estimated across a genome using Marey maps.

BugReports:

https://github.com/lbbe-software/MareyMap/issues

URL:

https://lbbe.univ-lyon1.fr/fr/mareymap https://lbbe-shiny.univ-lyon1.fr/MareyMapOnline/

LazyData:

Encoding:

UTF-8

NeedsCompilation:

Packaged:

2025-04-07 10:50:43 UTC; siberchicot

Author:

Gabriel Marais

[aut], Clément Rezvoy [aut], Delphine Charif [aut], Laurent Gueguen [aut], Aurélie Siberchicot

[ctb, cre]

Maintainer:

Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>

Repository:

CRAN

Date/Publication:

2025-04-07 11:00:02 UTC

The marey map for the species Arabidopsis thaliana

Description

A marey map is an interpolation between genetical and physical maps of a mapomosome. This data file contains marey map for the species Arabidopsis thaliana. This map is held into an object of class MapSet.

Usage

data(Arabidopsis_thaliana)

Format

Arabidopsis_thaliana contains an object of the class MapSet-class. The maps inside this object (objects of the class MareyMap-class) can be accessed using the operator "[[" (see example) This set contains 5 maps called "Chromosome 1", ..., "Chromosome 5".

Author(s)

Aurélie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Clément Rezvoy

Source

The physical positions were also recorded for those genetic markers that have both been mapped to the Recombinant Inbred (RI) recombination map (see https://arabidopsis.info/), and have been precisely physically mapped on the basis of flanking sequence, using the marker position information from TAIR. (release 1). Wright SI, Agrawal N, Bureau TE. Effects of recombination rate and gene density on transposable element distributions in Arabidopsis thaliana.Genome Res. 2003 Aug;13(8):1897-903.

Examples

#data(Arabidopsis_thaliana)
#map <- Arabidopsis_thaliana[["Chromosome 1"]]
#plot(map)
#names(Arabidopsis_thaliana@maps)

The marey map for the species Caenorhabditis_elegans

Description

A marey map is an interpolation between genetical and physical maps of a mapomosome. This data file contains marey map for the species Caenorhabditis_elegans. This map is held into an object of class MapSet.

Usage

data(Caenorhabditis_elegans)

Format

Caenorhabditis_elegans contains an object of the class MapSet-class. The maps inside this object (objects of the class MareyMap-class) can be accessed using the operator "[[" (see example) This set contains 6 maps called "I", "II", "III", "IV", "V" and "X".

Author(s)

Aurélie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Clément Rezvoy

Source

Wormbase Release WS160, https://wormbase.org//

Examples

data(Caenorhabditis_elegans)
map <- Caenorhabditis_elegans[["I"]]
plot(map)
names(Caenorhabditis_elegans@maps)

The marey map for the species Drosophila melanogaster

Description

A marey map is an interpolation between genetical and physical maps of a mapomosome. This data file contains marey map for the species Drosophila melanogaster. This map is held into an object of class MapSet.

Usage

data(Drosophila_melanogaster)

Format

Drosophila_melanogaster contains an object of the class MapSet-class. The maps inside this object (objects of the class MareyMap-class) can be accessed using the operator "[[" (see example) This set contains 6 maps called "2L", "2R", "3L", "3R", "4", "X".

Author(s)

Aurélie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Clément Rezvoy

Source

2nd release of D. mel genome, v 01/1998 Flybase. Marais G, Piganeau G.Hill-Robertson interference is a minor determinant of variations in codon bias across Drosophila melanogaster and Caenorhabditis elegans genomes. Mol Biol Evol. 2002 Sep;19(9):1399-406.

Examples

data(Drosophila_melanogaster)
map <- Drosophila_melanogaster[["2L"]]
plot(map)
names(Drosophila_melanogaster@maps)

The marey map for the species Homo sapiens (female, male and mean of the two)

Description

A marey map is an interpolation between genetical and physical maps of a mapomosome. This data file contains marey map for the species Homo sapiens. This map is held into an object of class MapSet.

Usage

data(Homo_sapiens_mean)

Format

Homo sapiens (female, male and mean) contains an object of the class MapSet-class. The maps inside this object (objects of the class MareyMap-class) can be accessed using the operator "[[" (see example) Each of the 3 sets (female, male and mean) contains 22 maps called "Chromosome 01", ... , "Chromosome 22".

Author(s)

Aurélie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Clément Rezvoy

Source

Rutgers Combined Linkage-Physical Maps, version 2.0 (Build 35). Xiangyang Komg and Tara Matise 12/08/2004

Examples

data(Homo_sapiens_female)
map <- Homo_sapiens_female[["Chromosome 01"]]
plot(map)
names(Homo_sapiens_female@maps)

Class "Interpolation"

Description

This class serves as a base for interpolation methods. Although it is not defined as virtual for technical reason, it should not be used as is and is only useful after having been extended.

Objects from the Class

Objects from the class should not be created

Slots

name:: Object of class "character" holding the name of the interpolation
color:: Object of class "character" holding the name or the code (#RRGGBB) of the color of the interpolation on the plot
physicalPositions:: Object of class "vector" holding the valid physical position of the map on which the interpolation is calculated. This redundancy is necessary to cary out the plotting of the map.
rates:: Object of class "vector" holding the local recombination rate estimations at the location of each markers.
visible:: Object of class "logical", whether or not the interpolation should be plotted
persistent:: Object of class "logical", whether or not the interpolation should be saved when the map is saved to text file.

Methods

argList: signature(object = "Interpolation"): This function is used in the function createList (c.f. code examples).
color<-: signature(object = "Interpolation"): changes the color of the interpolation.
color: signature(object = "Interpolation"): returns the color of the interpolation.
interpolate: signature(object = "Interpolation", map = "MareyMap"): recalculate the interpolation.
name<-: signature(object = "Interpolation"): changes the name of the interpolation.
name: signature(object = "Interpolation"): returns the name of the interpolation.
persistent<-: signature(object = "Interpolation"): changes the persistence state of the interpolation.
persistent: signature(object = "Interpolation"): returns the persistence state of the interpolation.
plotModel: signature(object = "Interpolation"): this function plots only the model of the marey map calculated by the method.
plotRate: signature(object = "Interpolation"): this function plots the recombination rates calculated by the method.
query: signature(object = "Interpolation", pos = "integer"): returns the recombination rate calculated by this method on a given location on the sequence.
rates<-: signature(object = "Interpolation"): replaces the rates with a new vector.
rates: signature(object = "Interpolation"): returns the rates of the interpolation.
userParam: signature(object = "Interpolation"): function returning information about the parameters modifiable by the user (c.f. code example.)
visible<-: signature(object = "Interpolation"): changes the visibility of the interpolation.
visible: signature(object = "Interpolation"): returns the visibility of the interpolation

Author(s)

Aurélie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Clément Rezvoy

Class "InterpolationParam"

Description

Class holding informations about a parameter of an interpolation method. This class is used in the function userParam,Interpolation-method. These informations are used by the GUI to dynamically create the dialog to modify this parameter.

Objects from the Class

Objects can be created by calls of the form new("InterpolationParam", ...) or using the methodInterpolationParam().

Slots

paramName:: Object of class "character" holding the name of the parameter.
paramType:: Object of class "character" holding the type of the parameter, currently supported parameter types are: logical, numeric, integer and color.
paramDesc:: Object of class "character" giving a small description of the parameter's signification.
paramDefault:: Object of class "ANY", default value for the parameter.
paramValues:: Object of class "vector" containing the set of valid values for the parameter (can be NULL).
paramMin:: Object of class "ANY", a minimum value for the parameter, or minimal string length if the parameter is of type character
paramMax:: Object of class "ANY" , a minimum value for the parameter, or maximum string length if the parameter is of type character
paramFun:: Object of class "character", the nae of function that is to be called to update the parameter's value. ex if paramFun is foo the parameter's value will be set using foo(interpolation)<-new_value

Methods

paramDefault<-: signature(object = "InterpolationParam"): ...
paramDefault: signature(object = "InterpolationParam"): ...
paramDesc<-: signature(object = "InterpolationParam", value = "character"): ...
paramDesc: signature(object = "InterpolationParam"): ...
paramFun<-: signature(object = "InterpolationParam", value = "character"): ...
paramFun: signature(object = "InterpolationParam"): ...
paramMax<-: signature(object = "InterpolationParam"): ...
paramMax: signature(object = "InterpolationParam"): ...
paramMin<-: signature(object = "InterpolationParam"): ...
paramMin: signature(object = "InterpolationParam"): ...
paramName<-: signature(object = "InterpolationParam", value = "character"): ...
paramName: signature(object = "InterpolationParam"): ...
paramType<-: signature(object = "InterpolationParam", value = "character"): ...
paramType: signature(object = "InterpolationParam"): ...
paramValues<-: signature(object = "InterpolationParam", value = "vector"): ...
paramValues: signature(object = "InterpolationParam"): ...

Author(s)

Aurélie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Clément Rezvoy

Examples

  nam <- InterpolationParam()
	paramName(nam) <- "name"
	paramDesc(nam) <- "The name of the interpolation.\n"
	paramType(nam) <- "character"
	paramDefault(nam) <- "default name"
	paramMin(nam) <- 1
	paramMax(nam) <- NULL	
	paramFun(nam) <- "name"

	vis <- InterpolationParam()
	paramName(vis) <- "visible"
	paramDesc(vis) <- "Whether the line is visible on the plot or not"
	paramType(vis) <- "logical"
	paramDefault(vis) <- TRUE
	paramFun(vis) <- "visible"
	
	sav <- InterpolationParam()
	paramName(sav) <- "persistent"
	paramDesc(sav) <- "Indicate if the interpolation is to be be kept \n\
  when the map is saved to text file"
	paramType(sav) <- "logical"
	paramDefault(sav) <- TRUE
	paramFun(sav) <- "persistent"
	
	col <- InterpolationParam()
	paramName(col) <- "line color"
	paramDesc(col) <- "color of the line"
	paramType(col) <- "color"
	paramDefault(col) <- "#000000"
	paramFun(col) <- "color"

Methods for Function InterpolationParam in Package 'MareyMap'

Description

constructor for class InterpolationParam-class in package MareyMap

Methods

dummy = "missing": default constructor.

Author(s)

Aurélie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Clément Rezvoy

Class "MMLoess". Interpolation method plug-in for MareyMap

Description

This packages provides an interpolation method that estimates the recombination rates using loess. For more details on how this method works, see loess.

Objects from the Class

Objects can be created by calls of the form new("MMLoess", ...) or simply by calling MMLoess().

Slots

span:: Object of class "numeric", parameters that controls the degree of smoothing.
degree:: Object of class "integer", the degree of the polynomials to be used, up to 2.
model:: Object of class "ANY"
name:: Object of class "character", name of the interpolation.
color:: Object of class "character", color of the interpolation on the map.
physicalPositions:: Object of class "vector", physical positions of the markers of the map on which the interpolation is calculated.
rates:: Object of class "vector", the local estimation of the recombination rate at the position of each markers.
visible:: Object of class "logical", whether the interpolation should be plotted or not.
persistent:: Object of class "logical", whether the interpolation should be saved along with the map in the text file

Extends

Class "Interpolation", directly.

Methods

createOrder: signature(object = "MMLoess"): see Interpolation-class.
degree<-: signature(object = "MMLoess"): changes the degree of the polynomials.
degree: signature(object = "MMLoess"): returns the degree of the polynomials.
interpolate: signature(object = "MMLoess", map = "MareyMap"): see Interpolation-class.
plotModel: signature(object = "MMLoess"): see Interpolation-class.
plotRate: signature(object = "MMLoess"): see Interpolation-class.
query: signature(object = "MMLoess", pos = "numeric"): see Interpolation-class.
span<-: signature(object = "MMLoess"): changes the value of the span.
span: signature(object = "MMLoess"): returns the value of the span.
userParam: signature(object = "MMLoess"): see Interpolation-class.

Author(s)

Aurélie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Clément Rezvoy

Examples

data(Homo_sapiens_male)
chr7 <- Homo_sapiens_male[["Chromosome 07"]]
itr1 <- MMLoess()
color(itr1) <- "red"
span(itr1) <- 0.05
chr7 <- chr7 + itr1

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
geneticalDistances:

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)

Aurélie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Clément Rezvoy

Examples

data(Homo_sapiens_mean)
human7 <- Homo_sapiens_mean[["Chromosome 07"]]
itr1 <- MMSlidingWindow()
color(itr1) <- "red"
size(itr1) <- 5000000
shift(itr1) <- 1000000
human7 <- human7 + itr1
plot(human7)

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.

Author(s)

Aurélie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Clément Rezvoy

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)

Class "MapCollection"

Description

This class holds several MareyMap-class objects organised in sets (using MapSet-class object).

Objects from the Class

Objects can be created by calls of the form new("MapCollection", ...) or using the function MapCollection. You may as well use the default collection provided by the package (as data()).

Slots

sets:: Object of class "list" containing a MapSet-class for each set$* of the collection.

Methods

[: signature(x = "MapCollection"): ...
[[<-: signature(x = "MapCollection", i = "ANY", j = "ANY", value = "MapSet"): ...
[[<-: signature(x = "MapCollection", i = "ANY", j = "ANY", value = "MareyMap"): ...
[[: signature(x = "MapCollection"): obtain the MapSet corresponding to a set name
$: signature(x = "MapCollection"): subset by set name
+: signature(e1 = "MapCollection", e2 = "MareyMap"): adds a map to the collection
+: signature(e1 = "MapCollection", e2 = "MapSet"): adds a set t the collection
-: signature(e1 = "MapCollection", e2 = "character"): removes the map named e2 from the object e1.
coerce: signature(from = "MapCollection", to = "data.frame"): --> as(object,"data.frame")
setNames: signature(object = "MapCollection"): returns the list of the names of all the sets present in the collection
length: signature(object = "MapCollection"): returns the length of the collection
textFile: signature(object = "MapCollection", file = "character"): Writes the content of the collection to text file text.

Author(s)

Aurélie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Clément Rezvoy

Examples

data(Homo_sapiens_mean)
map1 <- Homo_sapiens_mean[["Chromosome 01"]]
# do some useful changes to the map...
mapName(map1)<- "Chrom 1 (modified)"

Constructor for class MapCollection

Description

Creates an object of class MapCollection

Methods

x = "missing": Default constructor.

Author(s)

Aurélie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Clément Rezvoy

Class "MapSet"

Description

This class is a collection of MareyMap for a given set. Not that useful on its own, it is used for internal organization inside a MapCollection

Objects from the Class

Objects can be created by calls of the form new("MapSet", ...). Or using the function MapSet().

Slots

maps:: Object of class "list" containing all the MareyMap of the set.
setName:: Object of class "character" containing the name of the set

Methods

[: signature(x = "MapSet"): returns a map from the list
[[<-: signature(x = "MapSet", i = "ANY", j = "ANY", value = "MareyMap"): replaces a map in the list with a new one
[[: signature(x = "MapSet"): returns a map from the list.
$: signature(x = "MapSet"): access a map by name in the list.
+: signature(e1 = "MapSet", e2 = "MareyMap"): adds a map to the collection.
-: signature(e1 = "MapSet", e2 = "character"): removes the map named e2 from the object e1.
coerce: signature(from = "MapSet", to = "data.frame"): converts the specieMaps object into a data.frame.
mapNames: signature(object = "MapSet"): returns a vector containing the names of all the maps.
setName<-: signature(object = "MapSet", value = "character"): changes the name of the set. Also changes the named of all MareyMap objects inside the list.
setName: signature(object = "MapSet"): returns the name of the set.
length: signature(object = "MapCollection"): returns the length of the set
textFile: signature(object = "MapSet", file = "character"): Writes the content of the MapSet object to file.

Author(s)

Aurélie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Clément Rezvoy

Examples

data(Homo_sapiens_mean)
set <- Homo_sapiens_mean
setName(set) <- "Human"
set[["Chromosome 01"]]

Constructor for the class MapSet.

Description

Creates an object of the class MapSet.

Methods

set_name = "character": creates a new object of the class MapSet with the name set_name.

Author(s)

Aurélie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Clément Rezvoy

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 aurelie.siberchicot@univ-lyon1.fr and Clément Rezvoy

Examples

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

Constructor for object of the class MareyMap.

Description

Creates an object of the class MareyMap-class.

Methods

data_table = "missing", column_names = "missing", set_name = "missing", map_name = "missing": Default constructor
data_table = "data.frame": fill the class using the provided data.frame

Author(s)

Aurélie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Clément Rezvoy

Methods for function argList in package 'MareyMap'

Description

Methods for function argList in package MareyMap returns the argument list for object

Methods

object = "Interpolation": returns the basic interpolation parameters (for use in createOrder)

Author(s)

Aurélie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Clément Rezvoy

Accessors for slot color in package 'MareyMap'

Description

Methods for function color in package MareyMap

Methods

object = "Interpolation": Returns or sets the value of the slot color in the interpolation object

Author(s)

Aurélie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Clément Rezvoy

createOrder

Description

Returns a character containing the code to recreate the object as it is at the moment of the call (e.g. "new(objCLass, arg1=...)")

Methods

object = "MMSlidingWindow": createOrder for method MMSlidingWindow
object = "MMLoess": createOrder for method MMLoess
object = "MMSpline3": createOrder for method MMSpline3

Author(s)

Aurélie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Clément Rezvoy

Accessors for slot geneticDistances

Description

Methods for function geneticDistances in package MareyMap

Methods

object = "MareyMap": returns or set the value of the slot geneticDistances in MareyMap

Author(s)

Aurélie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Clément Rezvoy

returns a list of interpolation methods.

Description

returns the list of the interpolation methods present in the interpolation register.

Methods

dummy = "missing": default method.

Author(s)

Aurélie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Clément Rezvoy

interpolate

Description

performs an interpolation on map using the interpolation method provided by object

Methods

object = "Interpolation", map = "MareyMap": DO NOT USE in an 'real' programming language, this would be a virtual function
object = "MMSlidingWindow", map = "MareyMap": interpolate using sliding windows
object = "MMLoess", map = "MareyMap": interpolate using loess
object = "MMSpline3", map = "MareyMap": interpolate using cubic splines.

Author(s)

Aurélie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Clément Rezvoy

set or returns an interpolation.

Description

Methods for function interpolation in package MareyMap

Methods

object = "MareyMap", inter_name = "character": set or returns the interpolation inter_name in object MareyMap-class

Author(s)

Aurélie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Clément Rezvoy

accessors for slot interpolations

Description

set or get the value of the slot interpolation in object

Methods

object = "MareyMap": set or get slot interpolations in MareyMap-class

Author(s)

Aurélie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Clément Rezvoy

accessors for the slot mapName

Description

Set or get the value of the slot mapName in object.

Methods

object = "MareyMap": Set or get the value of the slot mapName in object.

Author(s)

Aurélie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Clément Rezvoy

mapNames

Description

Returns the names of the maps contained in object.

Methods

object = "MapSet": Returns the names of the maps contained in MapSet

Author(s)

Aurélie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Clément Rezvoy

Accessors for the class markerNames.

Description

Get or Set slot markerNames in object.

Methods

object = "MareyMap": Get or Set slot markerNames in MareyMap.

Author(s)

Aurélie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Clément Rezvoy

accessors for slot markerValidity

Description

Get or set the value of the slot MarkerValidity in object.

Methods

object = "MareyMap": Get or set the value of the slot MarkerValidity in MareyMap.

Author(s)

Aurélie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Clément Rezvoy

Accessor for slot name.

Description

Get or set the value of the slot name in object

Methods

object = "Interpolation": Get or set the value of the slot name in Interpolation.

Author(s)

Aurélie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Clément Rezvoy

Accessors for slot paramDefault

Description

Get or set the value of the slot paramDefault in object.

Methods

object = "InterpolationParam": Get or set the value of the slot paramDefault in MareyMap-class.

Author(s)

Aurélie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Clément Rezvoy

Accessors for the slot paramDesc

Description

Accessors for the slot paramDesc in object

Methods

object = "InterpolationParam": Accessors for the slot paramDesc in InterpolationParam

Author(s)

Aurélie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Clément Rezvoy

accessors for the slot paramFun

Description

Get or set the value of the slot paramFun in object

Methods

object = "InterpolationParam": Get or set the value of the slot paramFun in InterpolationParam-class.

Author(s)

Aurélie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Clément Rezvoy

Accessors for the slot paramMax.

Description

Get or set the value of the slot paramMax in object.

Methods

object = "InterpolationParam": Get or set the value of the slot paramMax in InterpolationParam.

Author(s)

Aurélie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Clément Rezvoy

Accessors for slot paramMin.

Description

Get or set the value of the parameter paramMin in object.

Methods

object = "InterpolationParam": Get or set the value of the parameter paramMin in InterpolationParam.

Author(s)

Aurélie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Clément Rezvoy

Accessors for the slot paramName.

Description

Get or set the value of the slot paramName in object.

Methods

object = "InterpolationParam": Get or set the value of the slot paramName in InterpolationParam.

Author(s)

Aurélie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Clément Rezvoy

Accessors for the slot paramType.

Description

Get or set the value of the slot paramType in object.

Methods

object = "InterpolationParam": Get or set the value of the slot paramType in InterpolationParam.

Author(s)

Aurélie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Clément Rezvoy

Accessor for the slot paramValues.

Description

Get or set the value of the slot paramValues in object.

Methods

object = "InterpolationParam": Get or set the value of the slot paramValues in InterpolationParam.

Author(s)

Aurélie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Clément Rezvoy

Accessors for the slot persistent.

Description

Get or set the value of the slot persistent in object.

Methods

object = "Interpolation": Get or set the value of the slot persistent in Interpolation.

Author(s)

Aurélie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Clément Rezvoy

Accessors for the slot physicalPositions

Description

Get or set the value of the slot physicalPositions object

Methods

object = "MareyMap": Get or set the value of the slot physicalPositions MareyMap-class

Author(s)

Aurélie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Clément Rezvoy

plotMarkers

Description

Plots the markers contained in object.

Methods

object = "MareyMap": Plots the markers of the map MareyMap

Author(s)

Aurélie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Clément Rezvoy

plotModel

Description

Plot the model of object

Methods

object = "Interpolation": Default function, plots nothing
object = "MMSlidingWindow": Plots the model of an interpolation of type MMSlidingWindow
object = "MMLoess": Plots the model of an interpolation of type MMLoess-class
object = "MMSpline3": Plots the model of an interpolation of type MMSpline3-class

Author(s)

Aurélie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Clément Rezvoy

plotModels

Description

plot models from object

Methods

object = "MareyMap": Calls plotModel on all the interpolation defined on the MareyMap.

Author(s)

Aurélie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Clément Rezvoy

plotRate

Description

Plots the variation of the recombination rate as calculated by object

Methods

object = "Interpolation": Plots the variation of the recombination rate as calculated by the Interpolation.
object = "MMSlidingWindow": Plots the variation of the recombination rate as calculated by MMSlidingWindow.
object = "MMLoess": Plots the variation of the recombination rate as calculated by MMLoess.
object = "MMSpline3": Plots the variation of the recombination rate as calculated by MMSpline3.

Author(s)

Aurélie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Clément Rezvoy

plotRates

Description

Plots the variations of the recombination rate as calculated by all the interpolations defined on the object.

Methods

object = "MareyMap": Plots the variations of the recombination rate as calculated by all the interpolations defined on the MareyMap.

Author(s)

Aurélie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Clément Rezvoy

Methods for Function query

Description

query an object for a given (or several) position(s).

Methods

object = "Interpolation", pos = "integer": Default method.
object = "MareyMap", pos = "numeric": Query the local recombination rate as calculated by all the Interpolation defined on the map.
object = "MMSlidingWindow", pos = "numeric": Query the local recombination rate as calculated by MMSlidingWindow.
object = "MMLoess", pos = "numeric": Query the local recombination rate as calculated by MMLoess.
object = "MMSpline3", pos = "numeric": Query the local recombination rate as calculated by MMSpline3.

Author(s)

Aurélie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Clément Rezvoy

Accessors for the slot rates

Description

Get or set the value of the slot rates in object

Methods

object = "Interpolation": Get or set the value of the slot rates in Interpolation.

Author(s)

Aurélie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Clément Rezvoy

registerInterpolationMethods

Description

Adds an Interpolation method to the interpolation register.

Methods

name = "character", classname = "character": Register an interpolation method with a given name and a contructor function classname.

Author(s)

Aurélie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Clément Rezvoy

removeMarker

Description

Removes a marker from an object

Methods

object = "MareyMap", value = "integer": Removes the marker number value from a MareyMap-class.

Author(s)

Aurélie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Clément Rezvoy

Accessors for the slot setName.

Description

Get or set the value of the slot setName in object.

Methods

object = "MareyMap": Get or set the value of the slot setName in MareyMap.
object = "MapSet": Get or set the value of the slot setName in MapSet.

Author(s)

Aurélie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Clément Rezvoy

setNames

Description

returns the names of the set contained in object.

Methods

object = "MapCollection": Returns the name of the set contained in MapCollection.

Author(s)

Aurélie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Clément Rezvoy

MareyMapGUI launcher

Description

launches the graphical user interface of MareyMapGUI

Methods

dummy = "missing": Default method.

Author(s)

Aurélie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Clément Rezvoy

textFile

Description

Writes object to text file.

Methods

object = "MapCollection", file = "character": Writes a MapCollection to text file.
object = "MareyMap", file = "character": Writes a MareyMap to text file.
object = "MapSet", file = "character": Writes a MapSet to text file.

Author(s)

Aurélie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Clément Rezvoy

userParam

Description

Returns information about the parameters modifiable by the user in object

Methods

object = "Interpolation": Returns information about the parameters modifiable by the user in Interpolation
object = "MMSlidingWindow": Returns information about the parameters modifiable by the user in MMSlidingWindow
object = "MMLoess": Returns information about the parameters modifiable by the user in MMLoess
object = "MMSpline3": Returns information about the parameters modifiable by the user in MMSpline3

Author(s)

Aurélie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Clément Rezvoy

validPositions

Description

Returns the positions of object which are valid.

Methods

object = "MareyMap": Returns the physical positions of MareyMap which are valid.

Author(s)

Aurélie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Clément Rezvoy

Accessors for the slot visible

Description

Get of set the value of the slot visible in object

Methods

object = "Interpolation": Get of set the value of the slot visible in Interpolation-class

Author(s)

Aurélie Siberchicot aurelie.siberchicot@univ-lyon1.fr and Clément Rezvoy

The marey map for the species Arabidopsis thaliana

Description

Usage

Format

Author(s)

Source

Examples

The marey map for the species Caenorhabditis_elegans

Description

Usage

Format

Author(s)

Source

Examples

The marey map for the species Drosophila melanogaster

Description

Usage

Format

Author(s)

Source

Examples

The marey map for the species Homo sapiens (female, male and mean of the two)

Description

Usage

Format

Author(s)

Source

Examples

Class "Interpolation"

Description

Objects from the Class

Slots

Methods

Author(s)

See Also

Class "InterpolationParam"

Description

Objects from the Class

Slots

Methods

Author(s)

See Also

Examples

Methods for Function InterpolationParam in Package 'MareyMap'

Description

Methods

Author(s)

See Also

Class "MMLoess". Interpolation method plug-in for MareyMap

Description

Objects from the Class

Slots

Extends

Methods

Author(s)

See Also

Examples

Class "MMSlidingWindow" Interpolation method plug-in for MareyMap

Description

Objects from the Class

Slots

Extends

Methods

Author(s)

See Also

Examples

Class "MMSpline3" Interpolation using cubic splines

Description

Objects from the Class

Slots

Extends

Methods

Author(s)

See Also

Examples

Class "MapCollection"

Description

Objects from the Class

Slots

Methods