| Title: | Estimation of Meiotic Recombination Rates Using Marey Maps |
|---|---|
| Description: | Local recombination rates are graphically estimated across a genome using Marey maps. |
| Authors: | Aurélie Siberchicot, Clément Rezvoy, Delphine Charif, Laurent Gueguen and Gabriel Marais |
| Maintainer: | Aurélie Siberchicot <[email protected]> |
| License: | GPL (>= 2) |
| Version: | 1.3.7 |
| Built: | 2024-09-17 05:12:05 UTC |
| Source: | https://github.com/lbbe-software/mareymap |
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.
data(Arabidopsis_thaliana)data(Arabidopsis_thaliana)
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".
Aurélie Siberchicot [email protected] and Clément Rezvoy
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.
#data(Arabidopsis_thaliana) #map <- Arabidopsis_thaliana[["Chromosome 1"]] #plot(map) #names(Arabidopsis_thaliana@maps)#data(Arabidopsis_thaliana) #map <- Arabidopsis_thaliana[["Chromosome 1"]] #plot(map) #names(Arabidopsis_thaliana@maps)
Methods for function argList in package MareyMap returns the argument list for object
returns the basic interpolation parameters (for use in createOrder)
Aurélie Siberchicot [email protected] and Clément Rezvoy
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.
data(Caenorhabditis_elegans)data(Caenorhabditis_elegans)
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".
Aurélie Siberchicot [email protected] and Clément Rezvoy
Wormbase Release WS160, https://wormbase.org//
data(Caenorhabditis_elegans) map <- Caenorhabditis_elegans[["I"]] plot(map) names(Caenorhabditis_elegans@maps)data(Caenorhabditis_elegans) map <- Caenorhabditis_elegans[["I"]] plot(map) names(Caenorhabditis_elegans@maps)
Methods for function color in package MareyMap
Returns or sets the value of the slot color in the interpolation object
Aurélie Siberchicot [email protected] and Clément Rezvoy
Returns a character containing the code to recreate the object as it is at the moment of the call (e.g. "new(objCLass, arg1=...)")
createOrder for method MMSlidingWindow
createOrder for method MMLoess
createOrder for method MMSpline3
Aurélie Siberchicot [email protected] and Clément Rezvoy
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.
data(Drosophila_melanogaster)data(Drosophila_melanogaster)
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".
Aurélie Siberchicot [email protected] and Clément Rezvoy
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.
data(Drosophila_melanogaster) map <- Drosophila_melanogaster[["2L"]] plot(map) names(Drosophila_melanogaster@maps)data(Drosophila_melanogaster) map <- Drosophila_melanogaster[["2L"]] plot(map) names(Drosophila_melanogaster@maps)
Methods for function geneticDistances in package MareyMap
returns or set the value of the slot geneticDistances in MareyMap
Aurélie Siberchicot [email protected] and Clément Rezvoy
returns the list of the interpolation methods present in the interpolation register.
default method.
Aurélie Siberchicot [email protected] and Clément Rezvoy
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.
data(Homo_sapiens_mean)data(Homo_sapiens_mean)
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".
Aurélie Siberchicot [email protected] and Clément Rezvoy
Rutgers Combined Linkage-Physical Maps, version 2.0 (Build 35). Xiangyang Komg and Tara Matise 12/08/2004
data(Homo_sapiens_female) map <- Homo_sapiens_female[["Chromosome 01"]] plot(map) names(Homo_sapiens_female@maps)data(Homo_sapiens_female) map <- Homo_sapiens_female[["Chromosome 01"]] plot(map) names(Homo_sapiens_female@maps)
performs an interpolation on map using the interpolation method provided by object
DO NOT USE in an 'real' programming language, this would be a virtual function
interpolate using sliding windows
interpolate using loess
interpolate using cubic splines.
Aurélie Siberchicot [email protected] and Clément Rezvoy
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 should not be created
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.
signature(object = "Interpolation"): This function is used in the function createList (c.f. code examples).
signature(object = "Interpolation"): changes the color of the interpolation.
signature(object = "Interpolation"): returns the color of the interpolation.
signature(object = "Interpolation", map = "MareyMap"): recalculate the interpolation.
signature(object = "Interpolation"): changes the name of the interpolation.
signature(object = "Interpolation"): returns the name of the interpolation.
signature(object = "Interpolation"): changes the persistence state of the interpolation.
signature(object = "Interpolation"): returns the persistence state of the interpolation.
signature(object = "Interpolation"): this function plots only the model of the marey map calculated by the method.
signature(object = "Interpolation"): this function plots the recombination rates calculated by the method.
signature(object = "Interpolation", pos = "integer"): returns the recombination rate calculated by this method on a given location on the sequence.
signature(object = "Interpolation"): replaces the rates with a new vector.
signature(object = "Interpolation"): returns the rates of the interpolation.
signature(object = "Interpolation"): function returning information about the parameters modifiable by the user (c.f. code example.)
signature(object = "Interpolation"): changes the visibility of the interpolation.
signature(object = "Interpolation"): returns the visibility of the interpolation
Aurélie Siberchicot [email protected] and Clément Rezvoy
InterpolationParam-class
MareyMap-class
Methods for function interpolation in package MareyMap
set or returns the interpolation inter_name in object MareyMap-class
Aurélie Siberchicot [email protected] and Clément Rezvoy
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 can be created by calls of the form new("InterpolationParam", ...) or using the methodInterpolationParam().
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
signature(object = "InterpolationParam"): ...
signature(object = "InterpolationParam"): ...
signature(object = "InterpolationParam", value = "character"): ...
signature(object = "InterpolationParam"): ...
signature(object = "InterpolationParam", value = "character"): ...
signature(object = "InterpolationParam"): ...
signature(object = "InterpolationParam"): ...
signature(object = "InterpolationParam"): ...
signature(object = "InterpolationParam"): ...
signature(object = "InterpolationParam"): ...
signature(object = "InterpolationParam", value = "character"): ...
signature(object = "InterpolationParam"): ...
signature(object = "InterpolationParam", value = "character"): ...
signature(object = "InterpolationParam"): ...
signature(object = "InterpolationParam", value = "vector"): ...
signature(object = "InterpolationParam"): ...
Aurélie Siberchicot [email protected] and Clément Rezvoy
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"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"
constructor for class InterpolationParam-class in package MareyMap
default constructor.
Aurélie Siberchicot [email protected] and Clément Rezvoy
link{InterpolationParam-class}
set or get the value of the slot interpolation in object
set or get slot interpolations in MareyMap-class
Aurélie Siberchicot [email protected] and Clément Rezvoy
This class holds several MareyMap-class objects organised in sets (using MapSet-class object).
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()).
sets:Object of class "list" containing a MapSet-class for each set$* of the collection.
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.
signature(from = "MapCollection", to = "data.frame"): --> as(object,"data.frame")
signature(object = "MapCollection"): returns the list of the names of all the sets present in the collection
signature(object = "MapCollection"): returns the length of the collection
signature(object = "MapCollection", file = "character"): Writes the content of the collection to text file text.
Aurélie Siberchicot [email protected] and Clément Rezvoy
data(Homo_sapiens_mean) map1 <- Homo_sapiens_mean[["Chromosome 01"]] # do some useful changes to the map... mapName(map1)<- "Chrom 1 (modified)"data(Homo_sapiens_mean) map1 <- Homo_sapiens_mean[["Chromosome 01"]] # do some useful changes to the map... mapName(map1)<- "Chrom 1 (modified)"
Creates an object of class MapCollection
Default constructor.
Aurélie Siberchicot [email protected] and Clément Rezvoy
Set or get the value of the slot mapName in object.
Set or get the value of the slot mapName in object.
Aurélie Siberchicot [email protected] and Clément Rezvoy
Returns the names of the maps contained in object.
Returns the names of the maps contained in MapSet
Aurélie Siberchicot [email protected] and Clément Rezvoy
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 can be created by calls of the form new("MapSet", ...). Or using the function MapSet().
maps:Object of class "list" containing all the MareyMap of the set.
setName:Object of class "character" containing the name of the set
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.
signature(from = "MapSet", to = "data.frame"): converts the specieMaps object into a data.frame.
signature(object = "MapSet"): returns a vector containing the names of all the maps.
signature(object = "MapSet", value = "character"): changes the name of the set. Also changes the named of all MareyMap objects inside the list.
signature(object = "MapSet"): returns the name of the set.
signature(object = "MapCollection"): returns the length of the set
signature(object = "MapSet", file = "character"): Writes the content of the MapSet object to file.
Aurélie Siberchicot [email protected] and Clément Rezvoy
MapCollection-class
MareyMap-class
data(Homo_sapiens_mean) set <- Homo_sapiens_mean setName(set) <- "Human" set[["Chromosome 01"]]data(Homo_sapiens_mean) set <- Homo_sapiens_mean setName(set) <- "Human" set[["Chromosome 01"]]
Creates an object of the class MapSet.
creates a new object of the class MapSet with the name set_name.
Aurélie Siberchicot [email protected] and Clément Rezvoy
The class holds the physical and genetic positions of a marey map
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)
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.
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
signature(from = "MareyMap", to = "data.frame"): convert the Marey map into a data.frame.
signature(from = "MareyMap", to = "NULL"): returns NULL
signature(from = "data.frame", to = "MareyMap"): create a MareyMap from a data.frame.
signature(object = "MareyMap"): replace the genetic distance with a new vector.
signature(object = "MareyMap"): returns the genetic distances of the markers
signature(object = "MareyMap", inter_name = "character", value = "Interpolation"): replaces the interpolation which name matches inter_name with the content of the parameter value.
signature(object = "MareyMap", inter_name = "character"): returns the interpolation which name matches inter_name.
signature(object = "MareyMap"): replace the list of interpolation with a new list.
signature(object = "MareyMap"): returns the list of interpolations.
signature(object = "MareyMap"): replaces the name of the map
signature(object = "MareyMap"): returns the name of the map
signature(object = "MareyMap"): replaces the marker names with a new vector of names
signature(object = "MareyMap"): returns a vector containing the names of the markers
signature(object = "MareyMap"): replaces the marker validity with a new vector
signature(object = "MareyMap"): returns a vector containing information about the validity of the markers
signature(object = "MareyMap"): replaces the vector of physical positions with a new vector
signature(object = "MareyMap"): returns a vector containing the physical positions of the markers
signature(x = "MareyMap", y = "missing"): plots the map as well as the interpolations (if any)
signature(object = "MareyMap"): plots only the markers of the map, without plotting the interpolations
signature(object = "MareyMap"): plot only the models of the interpolations
signature(object = "MareyMap"): plots only the recombination rates
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]]
signature(object = "MareyMap", value = "integer"): remove the marker number value.
signature(object = "MareyMap", value = "ANY"): replaces the name of the set with a new character.
signature(object = "MareyMap"): returns the name of the set.
signature(object = "MareyMap"):
signature(object = "MareyMap", file = "character"): Writes the map to text file.
vectors markerNames, physicalPositions, geneticDistances and markerValidity must always retain the same length.
Aurélie Siberchicot [email protected] and Clément Rezvoy
MapCollection-class
MapSet-class
data(Homo_sapiens_male) chr7 <- Homo_sapiens_male[["Chromosome 07"]] chr7 <- chr7 + MMLoess() par(mfrow = c(2, 1)) plotMarkers(chr7)data(Homo_sapiens_male) chr7 <- Homo_sapiens_male[["Chromosome 07"]] chr7 <- chr7 + MMLoess() par(mfrow = c(2, 1)) plotMarkers(chr7)
Creates an object of the class MareyMap-class.
Default constructor
fill the class using the provided data.frame
Aurélie Siberchicot [email protected] and Clément Rezvoy
Get or Set slot markerNames in object.
Get or Set slot markerNames in MareyMap.
Aurélie Siberchicot [email protected] and Clément Rezvoy
Get or set the value of the slot MarkerValidity in object.
Get or set the value of the slot MarkerValidity in MareyMap.
Aurélie Siberchicot [email protected] and Clément Rezvoy
This packages provides an interpolation method that estimates the recombination rates using loess.
For more details on how this method works, see loess.
Objects can be created by calls of the form new("MMLoess", ...) or simply by calling MMLoess().
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
Class "Interpolation", directly.
signature(object = "MMLoess"): see Interpolation-class.
signature(object = "MMLoess"): changes the degree of the polynomials.
signature(object = "MMLoess"): returns the degree of the polynomials.
signature(object = "MMLoess", map = "MareyMap"): see Interpolation-class.
signature(object = "MMLoess"): see Interpolation-class.
signature(object = "MMLoess"): see Interpolation-class.
signature(object = "MMLoess", pos = "numeric"): see Interpolation-class.
signature(object = "MMLoess"): changes the value of the span.
signature(object = "MMLoess"): returns the value of the span.
signature(object = "MMLoess"): see Interpolation-class.
Aurélie Siberchicot [email protected] and Clément Rezvoy
data(Homo_sapiens_male) chr7 <- Homo_sapiens_male[["Chromosome 07"]] itr1 <- MMLoess() color(itr1) <- "red" span(itr1) <- 0.05 chr7 <- chr7 + itr1data(Homo_sapiens_male) chr7 <- Homo_sapiens_male[["Chromosome 07"]] itr1 <- MMLoess() color(itr1) <- "red" span(itr1) <- 0.05 chr7 <- chr7 + itr1
This package provides an interpolation method that estimates the recombination rates using a sliding window approach.
Objects can be created by calls of the form new("MMSlidingWindow", ...) or using the method SlidingWindow().
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:Class "Interpolation", directly.
signature(object = "MMSlidingWindow"): see Interpolation-class
signature(object = "MMSlidingWindow", map = "MareyMap"): see Interpolation-class
signature(object = "MMSlidingWindow"): see Interpolation-class
signature(object = "MMSlidingWindow"): see Interpolation-class
signature(object = "MMSlidingWindow", pos = "numeric"): see Interpolation-class
signature(object = "MMSlidingWindow"): updates the value of the parameter shift
signature(object = "MMSlidingWindow"): returns the value of the parameter shift
signature(object = "MMSlidingWindow"): updates the value of the parameter size
signature(object = "MMSlidingWindow"): returns the value of the parameter size
signature(object = "MMSlidingWindow"): updates the value of the parameter threshold
signature(object = "MMSlidingWindow"): returns the value of the parameter threshold
signature(object = "MMSlidingWindow"): see Interpolation-class
Aurélie Siberchicot [email protected] and Clément Rezvoy
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)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)
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 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.
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.
Class "Interpolation", directly.
signature(object = "MMSpline3", value = "numeric"): Changes the value of the degree of freedom.
signature(object = "MMSpline3"): returns the value of the degree of freedom.
signature(object = "MMSpline3", value = "logical"): Turns on or off the generalized cross validation.
signature(object = "MMSpline3"): indicates whether the generalized cross validation is on or not.
signature(object = "MMSpline3"): see Interpolation-class
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
signature(object = "MMSpline3"): Plot the interpolation's model of the Marey curve.
signature(object = "MMSpline3"): Plots the variations of the recombination rates across a mapomosome.
signature(object = "MMSpline3", pos = "numeric"): query the estimation of the recombination rate in a specific position (or a vector of specific positions)
signature(object = "MMSpline3", value = "numeric"): Changes the value of the spar.
signature(object = "MMSpline3"): returns the value of the spar.
signature(object = "MMSpline3", value = "character"): Changes the type of smoothing to be used.
signature(object = "MMSpline3"): returns the smoothing method used.
signature(object = "MMSpline3"): returns informations about the user parameter, used by tcl/tk interface but not that useful for a command line user.
Aurélie Siberchicot [email protected] and Clément Rezvoy
smooth.spline
Interpolation-class
MareyMap-class
data(Homo_sapiens_mean) human7 <- Homo_sapiens_mean[["Chromosome 07"]] itr1 <- MMSpline3() color(itr1) <- "red" spar(itr1) <- 0.05 human7 <- human7 + itr1 plot(human7)data(Homo_sapiens_mean) human7 <- Homo_sapiens_mean[["Chromosome 07"]] itr1 <- MMSpline3() color(itr1) <- "red" spar(itr1) <- 0.05 human7 <- human7 + itr1 plot(human7)
Get or set the value of the slot name in object
Get or set the value of the slot name in Interpolation.
Aurélie Siberchicot [email protected] and Clément Rezvoy
Get or set the value of the slot paramDefault in object.
Get or set the value of the slot paramDefault in MareyMap-class.
Aurélie Siberchicot [email protected] and Clément Rezvoy
Accessors for the slot paramDesc in object
Accessors for the slot paramDesc in InterpolationParam
Aurélie Siberchicot [email protected] and Clément Rezvoy
Get or set the value of the slot paramFun in object
Get or set the value of the slot paramFun in InterpolationParam-class.
Aurélie Siberchicot [email protected] and Clément Rezvoy
Get or set the value of the slot paramMax in object.
Get or set the value of the slot paramMax in InterpolationParam.
Aurélie Siberchicot [email protected] and Clément Rezvoy
Get or set the value of the parameter paramMin in object.
Get or set the value of the parameter paramMin in InterpolationParam.
Aurélie Siberchicot [email protected] and Clément Rezvoy
Get or set the value of the slot paramName in object.
Get or set the value of the slot paramName in InterpolationParam.
Aurélie Siberchicot [email protected] and Clément Rezvoy
Get or set the value of the slot paramType in object.
Get or set the value of the slot paramType in InterpolationParam.
Aurélie Siberchicot [email protected] and Clément Rezvoy
Get or set the value of the slot paramValues in object.
Get or set the value of the slot paramValues in InterpolationParam.
Aurélie Siberchicot [email protected] and Clément Rezvoy
Get or set the value of the slot persistent in object.
Get or set the value of the slot persistent in Interpolation.
Aurélie Siberchicot [email protected] and Clément Rezvoy
Get or set the value of the slot physicalPositions object
Get or set the value of the slot physicalPositions MareyMap-class
Aurélie Siberchicot [email protected] and Clément Rezvoy
Plots the markers contained in object.
Plots the markers of the map MareyMap
Aurélie Siberchicot [email protected] and Clément Rezvoy
Plot the model of object
Default function, plots nothing
Plots the model of an interpolation of type MMSlidingWindow
Plots the model of an interpolation of type MMLoess-class
Plots the model of an interpolation of type MMSpline3-class
Aurélie Siberchicot [email protected] and Clément Rezvoy
plot models from object
Calls plotModel on all the interpolation defined on the MareyMap.
Aurélie Siberchicot [email protected] and Clément Rezvoy
Plots the variation of the recombination rate as calculated by object
Plots the variation of the recombination rate as calculated by the Interpolation.
Plots the variation of the recombination rate as calculated by MMSlidingWindow.
Plots the variation of the recombination rate as calculated by MMLoess.
Plots the variation of the recombination rate as calculated by MMSpline3.
Aurélie Siberchicot [email protected] and Clément Rezvoy
Plots the variations of the recombination rate as calculated by all the interpolations defined on the object.
Plots the variations of the recombination rate as calculated by all the interpolations defined on the MareyMap.
Aurélie Siberchicot [email protected] and Clément Rezvoy
query an object for a given (or several) position(s).
Default method.
Query the local recombination rate as calculated by all the Interpolation defined on the map.
Query the local recombination rate as calculated by MMSlidingWindow.
Query the local recombination rate as calculated by MMLoess.
Query the local recombination rate as calculated by MMSpline3.
Aurélie Siberchicot [email protected] and Clément Rezvoy
Get or set the value of the slot rates in object
Get or set the value of the slot rates in Interpolation.
Aurélie Siberchicot [email protected] and Clément Rezvoy
Adds an Interpolation method to the interpolation register.
Register an interpolation method with a given name and a contructor function classname.
Aurélie Siberchicot [email protected] and Clément Rezvoy
Removes a marker from an object
Removes the marker number value from a MareyMap-class.
Aurélie Siberchicot [email protected] and Clément Rezvoy
Get or set the value of the slot setName in object.
Get or set the value of the slot setName in MareyMap.
Get or set the value of the slot setName in MapSet.
Aurélie Siberchicot [email protected] and Clément Rezvoy
returns the names of the set contained in object.
Returns the name of the set contained in MapCollection.
Aurélie Siberchicot [email protected] and Clément Rezvoy
launches the graphical user interface of MareyMapGUI
Default method.
Aurélie Siberchicot [email protected] and Clément Rezvoy
Writes object to text file.
Writes a MapCollection to text file.
Writes a MareyMap to text file.
Writes a MapSet to text file.
Aurélie Siberchicot [email protected] and Clément Rezvoy
MareyMap-class
MapCollection-class
MapSet-class
Returns information about the parameters modifiable by the user in object
Returns information about the parameters modifiable by the user in Interpolation
Returns information about the parameters modifiable by the user in MMSlidingWindow
Returns information about the parameters modifiable by the user in MMLoess
Returns information about the parameters modifiable by the user in MMSpline3
Aurélie Siberchicot [email protected] and Clément Rezvoy
Interpolation-class
InterpolationParam-class
Returns the positions of object which are valid.
Returns the physical positions of MareyMap which are valid.
Aurélie Siberchicot [email protected] and Clément Rezvoy
Get of set the value of the slot visible in object
Get of set the value of the slot visible in Interpolation-class
Aurélie Siberchicot [email protected] and Clément Rezvoy