# Estimation of Meiotic Recombination Rates Using Marey Maps

## Documentation for package ‘MareyMap’ version 1.3.5

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

A C D G H I L M N P Q R S T U V misc

## -- A --

Arabidopsis_thaliana | The marey map for the species Arabidopsis thaliana
argList | Methods for function argList in package 'MareyMap'
argList-method | Class "Interpolation"
argList-methods | Methods for function argList in package 'MareyMap'

## -- C --

Caenorhabditis_elegans | The marey map for the species Caenorhabditis_elegans
coerce-method | Class "MapCollection"
coerce-method | Class "MareyMap"
coerce-method | Class "MapSet"
color | Accessors for slot color in package 'MareyMap'
color-method | Class "Interpolation"
color-methods | Accessors for slot color in package 'MareyMap'
color<- | Accessors for slot color in package 'MareyMap'
color<--method | Class "Interpolation"
color<--methods | Accessors for slot color in package 'MareyMap'
createOrder | createOrder
createOrder-method | Class "MMLoess". Interpolation method plug-in for MareyMap
createOrder-method | Class "MMSlidingWindow" Interpolation method plug-in for MareyMap
createOrder-method | Class "MMSpline3" Interpolation using cubic splines
createOrder-methods | createOrder

## -- D --

degree | Class "MMLoess". Interpolation method plug-in for MareyMap
degree-method | Class "MMLoess". Interpolation method plug-in for MareyMap
degree<- | Class "MMLoess". Interpolation method plug-in for MareyMap
degree<--method | Class "MMLoess". Interpolation method plug-in for MareyMap
df | Class "MMSpline3" Interpolation using cubic splines
df-method | Class "MMSpline3" Interpolation using cubic splines
df<- | Class "MMSpline3" Interpolation using cubic splines
df<--method | Class "MMSpline3" Interpolation using cubic splines
Drosophila_melanogaster | The marey map for the species Drosophila melanogaster

## -- G --

gcv | Class "MMSpline3" Interpolation using cubic splines
gcv-method | Class "MMSpline3" Interpolation using cubic splines
gcv<- | Class "MMSpline3" Interpolation using cubic splines
gcv<--method | Class "MMSpline3" Interpolation using cubic splines
geneticDistances | Accessors for slot geneticDistances
geneticDistances-method | Class "MareyMap"
geneticDistances-methods | Accessors for slot geneticDistances
geneticDistances<- | Accessors for slot geneticDistances
geneticDistances<--method | Class "MareyMap"
geneticDistances<--methods | Accessors for slot geneticDistances
getInterList | returns a list of interpolation methods.
getInterList-method | returns a list of interpolation methods.
getInterList-methods | returns a list of interpolation methods.

## -- H --

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

## -- I --

interpolate | interpolate
interpolate-method | Class "Interpolation"
interpolate-method | Class "MMLoess". Interpolation method plug-in for MareyMap
interpolate-method | Class "MMSlidingWindow" Interpolation method plug-in for MareyMap
interpolate-method | Class "MMSpline3" Interpolation using cubic splines
interpolate-methods | interpolate
Interpolation | Class "Interpolation"
interpolation | set or returns an interpolation.
Interpolation-class | Class "Interpolation"
interpolation-method | Class "MareyMap"
interpolation-methods | set or returns an interpolation.
interpolation<- | set or returns an interpolation.
interpolation<--method | Class "MareyMap"
interpolation<--methods | set or returns an interpolation.
InterpolationParam | Class "InterpolationParam"
InterpolationParam-class | Class "InterpolationParam"
InterpolationParam-method | Methods for Function InterpolationParam in Package 'MareyMap'
InterpolationParam-methods | Methods for Function InterpolationParam in Package 'MareyMap'
interpolations | accessors for slot interpolations
interpolations-method | Class "MareyMap"
interpolations-methods | accessors for slot interpolations
interpolations<- | accessors for slot interpolations
interpolations<--method | Class "MareyMap"
interpolations<--methods | accessors for slot interpolations

## -- L --

length-method | Class "MapCollection"
length-method | Class "MapSet"

## -- M --

MapCollection | Class "MapCollection"
MapCollection-class | Class "MapCollection"
MapCollection-method | Class "MapCollection"
MapCollection-methods | Constructor for class MapCollection
mapName | accessors for the slot mapName
mapName-method | Class "MareyMap"
mapName-methods | accessors for the slot mapName
mapName<- | accessors for the slot mapName
mapName<--method | Class "MareyMap"
mapName<--methods | accessors for the slot mapName
mapNames | mapNames
mapNames-method | Class "MapSet"
mapNames-methods | mapNames
MapSet | Class "MapSet"
MapSet-class | Class "MapSet"
MapSet-method | Constructor for the class MapSet.
MapSet-methods | Constructor for the class MapSet.
MareyMap | Class "MareyMap"
MareyMap-class | Class "MareyMap"
MareyMap-method | Class "MareyMap"
MareyMap-method | Constructor for object of the class MareyMap.
MareyMap-methods | Constructor for object of the class MareyMap.
markerNames | Accessors for the class markerNames.
markerNames-method | Class "MareyMap"
markerNames-methods | Accessors for the class markerNames.
markerNames<- | Accessors for the class markerNames.
markerNames<--method | Class "MareyMap"
markerNames<--methods | Accessors for the class markerNames.
markerValidity | accessors for slot markerValidity
markerValidity-method | Class "MareyMap"
markerValidity-methods | accessors for slot markerValidity
markerValidity<- | accessors for slot markerValidity
markerValidity<--method | Class "MareyMap"
markerValidity<--methods | accessors for slot markerValidity
MMLoess | Class "MMLoess". Interpolation method plug-in for MareyMap
MMLoess-class | Class "MMLoess". Interpolation method plug-in for MareyMap
MMLoess-method | Class "MMLoess". Interpolation method plug-in for MareyMap
MMLoess-methods | Class "MMLoess". Interpolation method plug-in for MareyMap
MMSlidingWindow | Class "MMSlidingWindow" Interpolation method plug-in for MareyMap
MMSlidingWindow-class | Class "MMSlidingWindow" Interpolation method plug-in for MareyMap
MMSlidingWindow-method | Class "MMSlidingWindow" Interpolation method plug-in for MareyMap
MMSlidingWindow-methods | Class "MMSlidingWindow" Interpolation method plug-in for MareyMap
MMSpline3 | Class "MMSpline3" Interpolation using cubic splines
MMSpline3-class | Class "MMSpline3" Interpolation using cubic splines
MMSpline3-method | Class "MMSpline3" Interpolation using cubic splines
MMSpline3-methods | Class "MMSpline3" Interpolation using cubic splines

## -- N --

name | Accessor for slot name.
name-method | Class "Interpolation"
name-methods | Accessor for slot name.
name<- | Accessor for slot name.
name<--method | Class "Interpolation"
name<--methods | Accessor for slot name.

## -- P --

paramDefault | Accessors for slot paramDefault
paramDefault-method | Class "InterpolationParam"
paramDefault-methods | Accessors for slot paramDefault
paramDefault<- | Accessors for slot paramDefault
paramDefault<--method | Class "InterpolationParam"
paramDefault<--methods | Accessors for slot paramDefault
paramDesc | Accessors for the slot paramDesc
paramDesc-method | Class "InterpolationParam"
paramDesc-methods | Accessors for the slot paramDesc
paramDesc<- | Accessors for the slot paramDesc
paramDesc<--method | Class "InterpolationParam"
paramDesc<--methods | Accessors for the slot paramDesc
paramFun | accessors for the slot paramFun
paramFun-method | Class "InterpolationParam"
paramFun-methods | accessors for the slot paramFun
paramFun<- | accessors for the slot paramFun
paramFun<--method | Class "InterpolationParam"
paramFun<--methods | accessors for the slot paramFun
paramMax | Accessors for the slot paramMax.
paramMax-method | Class "InterpolationParam"
paramMax-methods | Accessors for the slot paramMax.
paramMax<- | Accessors for the slot paramMax.
paramMax<--method | Class "InterpolationParam"
paramMax<--methods | Accessors for the slot paramMax.
paramMin | Accessors for slot paramMin.
paramMin-method | Class "InterpolationParam"
paramMin-methods | Accessors for slot paramMin.
paramMin<- | Accessors for slot paramMin.
paramMin<--method | Class "InterpolationParam"
paramMin<--methods | Accessors for slot paramMin.
paramName | Accessors for the slot paramName.
paramName-method | Class "InterpolationParam"
paramName-methods | Accessors for the slot paramName.
paramName<- | Accessors for the slot paramName.
paramName<--method | Class "InterpolationParam"
paramName<--methods | Accessors for the slot paramName.
paramType | Accessors for the slot paramType.
paramType-method | Class "InterpolationParam"
paramType-methods | Accessors for the slot paramType.
paramType<- | Accessors for the slot paramType.
paramType<--method | Class "InterpolationParam"
paramType<--methods | Accessors for the slot paramType.
paramValues | Accessor for the slot paramValues.
paramValues-method | Class "InterpolationParam"
paramValues-methods | Accessor for the slot paramValues.
paramValues<- | Accessor for the slot paramValues.
paramValues<--method | Class "InterpolationParam"
paramValues<--methods | Accessor for the slot paramValues.
persistent | Accessors for the slot persistent.
persistent-method | Class "Interpolation"
persistent-methods | Accessors for the slot persistent.
persistent<- | Accessors for the slot persistent.
persistent<--method | Class "Interpolation"
persistent<--methods | Accessors for the slot persistent.
physicalPositions | Accessors for the slot physicalPositions
physicalPositions-method | Class "MareyMap"
physicalPositions-methods | Accessors for the slot physicalPositions
physicalPositions<- | Accessors for the slot physicalPositions
physicalPositions<--method | Class "MareyMap"
physicalPositions<--methods | Accessors for the slot physicalPositions
plot-method | Class "Interpolation"
plot-method | Class "MMLoess". Interpolation method plug-in for MareyMap
plot-method | Class "MMSlidingWindow" Interpolation method plug-in for MareyMap
plot-method | Class "MMSpline3" Interpolation using cubic splines
plot-method | Class "MareyMap"
plotMarkers | plotMarkers
plotMarkers-method | Class "MareyMap"
plotMarkers-methods | plotMarkers
plotModel | plotModel
plotModel-method | Class "Interpolation"
plotModel-method | Class "MMLoess". Interpolation method plug-in for MareyMap
plotModel-method | Class "MMSlidingWindow" Interpolation method plug-in for MareyMap
plotModel-method | Class "MMSpline3" Interpolation using cubic splines
plotModel-methods | plotModel
plotModels | plotModels
plotModels-method | Class "MareyMap"
plotModels-methods | plotModels
plotRate | plotRate
plotRate-method | Class "Interpolation"
plotRate-method | Class "MMLoess". Interpolation method plug-in for MareyMap
plotRate-method | Class "MMSlidingWindow" Interpolation method plug-in for MareyMap
plotRate-method | Class "MMSpline3" Interpolation using cubic splines
plotRate-methods | plotRate
plotRates | plotRates
plotRates-method | Class "MareyMap"
plotRates-methods | plotRates

## -- Q --

query | Methods for Function query
query-method | Class "Interpolation"
query-method | Class "MMLoess". Interpolation method plug-in for MareyMap
query-method | Class "MMSlidingWindow" Interpolation method plug-in for MareyMap
query-method | Class "MMSpline3" Interpolation using cubic splines
query-method | Class "MareyMap"
query-methods | Methods for Function query

## -- R --

rates | Accessors for the slot rates
rates-method | Class "Interpolation"
rates-methods | Accessors for the slot rates
rates<- | Accessors for the slot rates
rates<--method | Class "Interpolation"
rates<--methods | Accessors for the slot rates
registerInterpolationMethod | registerInterpolationMethods
registerInterpolationMethod-method | registerInterpolationMethods
registerInterpolationMethod-methods | registerInterpolationMethods
removeMarker | removeMarker
removeMarker-method | Class "MareyMap"
removeMarker-methods | removeMarker

## -- S --

setName | Accessors for the slot setName.
setName-method | Class "MareyMap"
setName-method | Class "MapSet"
setName-methods | Accessors for the slot setName.
setName<- | Accessors for the slot setName.
setName<--method | Class "MareyMap"
setName<--method | Class "MapSet"
setName<--methods | Accessors for the slot setName.
setNames | setNames
setNames-method | Class "MapCollection"
setNames-methods | setNames
shift | Class "MMSlidingWindow" Interpolation method plug-in for MareyMap
shift-method | Class "MMSlidingWindow" Interpolation method plug-in for MareyMap
shift<- | Class "MMSlidingWindow" Interpolation method plug-in for MareyMap
shift<--method | Class "MMSlidingWindow" Interpolation method plug-in for MareyMap
size | Class "MMSlidingWindow" Interpolation method plug-in for MareyMap
size-method | Class "MMSlidingWindow" Interpolation method plug-in for MareyMap
size<- | Class "MMSlidingWindow" Interpolation method plug-in for MareyMap
size<--method | Class "MMSlidingWindow" Interpolation method plug-in for MareyMap
span | Class "MMLoess". Interpolation method plug-in for MareyMap
span-method | Class "MMLoess". Interpolation method plug-in for MareyMap
span<- | Class "MMLoess". Interpolation method plug-in for MareyMap
span<--method | Class "MMLoess". Interpolation method plug-in for MareyMap
spar | Class "MMSpline3" Interpolation using cubic splines
spar-method | Class "MMSpline3" Interpolation using cubic splines
spar<- | Class "MMSpline3" Interpolation using cubic splines
spar<--method | Class "MMSpline3" Interpolation using cubic splines
startMareyMapGUI | MareyMapGUI launcher
startMareyMapGUI-method | MareyMapGUI launcher
startMareyMapGUI-methods | MareyMapGUI launcher

## -- T --

textFile | textFile
textFile-method | Class "MapCollection"
textFile-method | Class "MareyMap"
textFile-method | Class "MapSet"
textFile-methods | textFile
threshold | Class "MMSlidingWindow" Interpolation method plug-in for MareyMap
threshold-method | Class "MMSlidingWindow" Interpolation method plug-in for MareyMap
threshold<- | Class "MMSlidingWindow" Interpolation method plug-in for MareyMap
threshold<--method | Class "MMSlidingWindow" Interpolation method plug-in for MareyMap
type | Class "MMSpline3" Interpolation using cubic splines
type-method | Class "MMSpline3" Interpolation using cubic splines
type<- | Class "MMSpline3" Interpolation using cubic splines
type<--method | Class "MMSpline3" Interpolation using cubic splines

## -- U --

userParam | userParam
userParam-method | Class "Interpolation"
userParam-method | Class "MMLoess". Interpolation method plug-in for MareyMap
userParam-method | Class "MMSlidingWindow" Interpolation method plug-in for MareyMap
userParam-method | Class "MMSpline3" Interpolation using cubic splines
userParam-methods | userParam

## -- V --

validPositions | validPositions
validPositions-method | Class "MareyMap"
validPositions-methods | validPositions
visible | Accessors for the slot visible
visible-method | Class "Interpolation"
visible-methods | Accessors for the slot visible
visible<- | Accessors for the slot visible
visible<--method | Class "Interpolation"
visible<--methods | Accessors for the slot visible

## -- misc --

$-method | Class "MapCollection"
$-method | Class "MapSet"
+-method | Class "MapCollection"
+-method | Class "MareyMap"
+-method | Class "MapSet"
--method | Class "MapCollection"
--method | Class "MapSet"
[-method | Class "MapCollection"
[-method | Class "MareyMap"
[-method | Class "MapSet"
[[-method | Class "MapCollection"
[[-method | Class "MareyMap"
[[-method | Class "MapSet"
[[<--method | Class "MapCollection"
[[<--method | Class "MareyMap"
[[<--method | Class "MapSet"