MareyMap: Estimation of Meiotic Recombination Rates Using Marey Maps
Version 1.3.3

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

Browse man pages Browse package API and functions Browse package files

AuthorAurélie Siberchicot, Clément Rezvoy, Delphine Charif, Laurent Gueguen and Gabriel Marais
Date of publication2016-11-15 12:08:22
MaintainerAurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>
LicenseGPL (>= 2)
Version1.3.3
URL https://lbbe.univ-lyon1.fr/-MareyMap-.html ; http://lbbe-shiny.univ-lyon1.fr/MareyMapOnline/
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("MareyMap")

Man pages

Arabidopsis_thaliana: The marey map for the species Arabidopsis thaliana
argList-methods: Methods for function argList in package 'MareyMap'
Caenorhabditis_elegans: The marey map for the species Caenorhabditis_elegans
color-methods: Accessors for slot color in package 'MareyMap'
createOrder-methods: createOrder
Drosophila_melanogaster: The marey map for the species Drosophila melanogaster
geneticDistances-methods: Accessors for slot geneticDistances
getInterList-methods: returns a list of interpolation methods.
Homo_sapiens: The marey map for the species Homo sapiens (female, male and...
interpolate-methods: interpolate
Interpolation-class: Class "Interpolation"
interpolation-methods: set or returns an interpolation.
InterpolationParam-class: Class "InterpolationParam"
InterpolationParam-methods: Methods for Function InterpolationParam in Package 'MareyMap'
interpolations-methods: accessors for slot interpolations
MapCollection-class: Class "MapCollection"
MapCollection-methods: Constructor for class MapCollection
mapName-methods: accessors for the slot mapName
mapNames-methods: mapNames
MareyMap-class: Class "MareyMap"
MareyMap-methods: Constructor for object of the class MareyMap.
markerNames-methods: Accessors for the class markerNames.
markerValidity-methods: accessors for slot markerValidity
MMLoess-class: Class "MMLoess". Interpolation method plug-in for MareyMap
MMSlidingWindow-class: Class "MMSlidingWindow" Interpolation method plug-in for...
MMSpline3-class: Class "MMSpline3" Interpolation using cubic splines
name-Methods: Accessor for slot name.
paramDefault-methods: Accessors for slot paramDefault
paramDesc-methods: Accessors for the slot paramDesc
paramFun-methods: accessors for the slot paramFun
paramMax-methods: Accessors for the slot paramMax.
paramMin-methods: Accessors for slot paramMin.
paramName-methods: Accessors for the slot paramName.
paramType-methods: Accessors for the slot paramType.
paramValues-methods: Accessor for the slot paramValues.
persistent-methods: Accessors for the slot persistent.
physicalPositions-methods: Accessors for the slot physicalPositions
plotMarkers-methods: plotMarkers
plotModel-methods: plotModel
plotModels-methods: plotModels
plotRate-methods: plotRate
plotRates-methods: plotRates
query-methods: Methods for Function query
rates-methods: Accessors for the slot rates
registerInterpolationMethod-methods: registerInterpolationMethods
removeMarker-methods: removeMarker
SpeciesMaps-class: Class "MapSet"
SpeciesMaps-methods: Constructor for the class MapSet.
speciesName-methods: Accessors for the slot setName.
speciesNames-methods: setNames
startMareyMapGUI-methods: MareyMapGUI launcher
textFile-methods: textFile
userParam-methods: userParam
validPositions-methods: validPositions
visible-methods: Accessors for the slot visible

Functions

$,MapCollection-method Man page
$,MapSet-method Man page
+,MapCollection,MapCollection-method Man page
+,MapCollection,MapSet-method Man page
+,MapCollection,MareyMap-method Man page
+,MapSet,MareyMap-method Man page
+,MareyMap,Interpolation-method Man page
-,MapCollection,character-method Man page
-,MapSet,character-method Man page
Arabidopsis_thaliana Man page
Caenorhabditis_elegans Man page
Drosophila_melanogaster Man page
Homo_sapiens_female Man page
Homo_sapiens_male Man page
Homo_sapiens_mean Man page
Interpolation Man page
Interpolation-class Man page
InterpolationParam Man page
InterpolationParam,missing-method Man page
InterpolationParam-class Man page
InterpolationParam-methods Man page
MMLoess Man page
MMLoess,missing-method Man page
MMLoess-class Man page
MMLoess-methods Man page
MMSlidingWindow Man page
MMSlidingWindow,missing-method Man page
MMSlidingWindow-class Man page
MMSlidingWindow-methods Man page
MMSpline3 Man page
MMSpline3,missing-method Man page
MMSpline3-class Man page
MMSpline3-methods Man page
MapCollection Man page
MapCollection,missing-method Man page
MapCollection-class Man page
MapCollection-methods Man page
MapSet Man page
MapSet,character-method Man page
MapSet-class Man page
MapSet-methods Man page
MareyMap Man page
MareyMap,data.frame,ANY,ANY,ANY-method Man page
MareyMap,missing,missing,missing,missing-method Man page
MareyMap-class Man page
MareyMap-methods Man page
[,MapCollection-method Man page
[,MapSet-method Man page
[,MareyMap-method Man page
[[,MapCollection-method Man page
[[,MapSet-method Man page
[[,MareyMap-method Man page
[[<-,MapCollection,ANY,ANY,MapSet-method Man page
[[<-,MapCollection,ANY,ANY,MareyMap-method Man page
[[<-,MapSet,ANY,ANY,MareyMap-method Man page
[[<-,MareyMap,ANY,ANY,ANY-method Man page
[[<-,MareyMap-method Man page
argList Man page
argList,Interpolation-method Man page
argList-methods Man page
coerce,MapCollection,data.frame-method Man page
coerce,MapSet,data.frame-method Man page
coerce,MareyMap,NULL-method Man page
coerce,MareyMap,data.frame-method Man page
coerce,data.frame,MareyMap-method Man page
color Man page
color,Interpolation-method Man page
color-methods Man page
color<- Man page
color<-,Interpolation-method Man page
color<--methods Man page
createOrder Man page
createOrder,MMLoess-method Man page
createOrder,MMSlidingWindow-method Man page
createOrder,MMSpline3-method Man page
createOrder-methods Man page
decodePosition Source code
degree Man page
degree,MMLoess-method Man page
degree<- Man page
degree<-,MMLoess-method Man page
df Man page
df,MMSpline3-method Man page
df<- Man page
df<-,MMSpline3,numeric-method Man page
gcv Man page
gcv,MMSpline3-method Man page
gcv<- Man page
gcv<-,MMSpline3,logical-method Man page
geneticDistances Man page
geneticDistances,MareyMap-method Man page
geneticDistances-methods Man page
geneticDistances<- Man page
geneticDistances<-,MareyMap-method Man page
geneticDistances<--methods Man page
getInterList Man page
getInterList,missing-method Man page
getInterList-methods Man page
interpolate Man page
interpolate,Interpolation,MareyMap-method Man page
interpolate,MMLoess,MareyMap-method Man page
interpolate,MMSlidingWindow,MareyMap-method Man page
interpolate,MMSpline3,MareyMap-method Man page
interpolate-methods Man page
interpolation Man page
interpolation,MareyMap,character-method Man page
interpolation-methods Man page
interpolation<- Man page
interpolation<-,MareyMap,character,Interpolation-method Man page
interpolation<--methods Man page
interpolations Man page
interpolations,MareyMap-method Man page
interpolations-methods Man page
interpolations<- Man page
interpolations<-,MareyMap-method Man page
interpolations<--methods Man page
length,MapCollection-method Man page
length,MapSet-method Man page
mapName Man page
mapName,MareyMap-method Man page
mapName-methods Man page
mapName<- Man page
mapName<-,MareyMap-method Man page
mapName<--methods Man page
mapNames Man page
mapNames,MapSet-method Man page
mapNames-methods Man page
markerNames Man page
markerNames,MareyMap-method Man page
markerNames-methods Man page
markerNames<- Man page
markerNames<-,MareyMap-method Man page
markerNames<--methods Man page
markerValidity Man page
markerValidity,MareyMap-method Man page
markerValidity-methods Man page
markerValidity<- Man page
markerValidity<-,MareyMap-method Man page
markerValidity<--methods Man page
name Man page
name,Interpolation-method Man page
name-methods Man page
name<- Man page
name<-,Interpolation-method Man page
name<--methods Man page
onMkrQuery Source code
onSelectPositionFile Source code
paramDefault Man page
paramDefault,InterpolationParam-method Man page
paramDefault-methods Man page
paramDefault<- Man page
paramDefault<-,InterpolationParam-method Man page
paramDefault<--methods Man page
paramDesc Man page
paramDesc,InterpolationParam-method Man page
paramDesc-methods Man page
paramDesc<- Man page
paramDesc<-,InterpolationParam,character-method Man page
paramDesc<--methods Man page
paramFun Man page
paramFun,InterpolationParam-method Man page
paramFun-methods Man page
paramFun<- Man page
paramFun<-,InterpolationParam,character-method Man page
paramFun<--methods Man page
paramMax Man page
paramMax,InterpolationParam-method Man page
paramMax-methods Man page
paramMax<- Man page
paramMax<-,InterpolationParam-method Man page
paramMax<--methods Man page
paramMin Man page
paramMin,InterpolationParam-method Man page
paramMin-methods Man page
paramMin<- Man page
paramMin<-,InterpolationParam-method Man page
paramMin<--methods Man page
paramName Man page
paramName,InterpolationParam-method Man page
paramName-methods Man page
paramName<- Man page
paramName<-,InterpolationParam,character-method Man page
paramName<--methods Man page
paramType Man page
paramType,InterpolationParam-method Man page
paramType-methods Man page
paramType<- Man page
paramType<-,InterpolationParam,character-method Man page
paramType<--methods Man page
paramValues Man page
paramValues,InterpolationParam-method Man page
paramValues-methods Man page
paramValues<- Man page
paramValues<-,InterpolationParam,vector-method Man page
paramValues<--methods Man page
persistent Man page
persistent,Interpolation-method Man page
persistent-methods Man page
persistent<- Man page
persistent<-,Interpolation-method Man page
persistent<--methods Man page
physicalPositions Man page
physicalPositions,MareyMap-method Man page
physicalPositions-methods Man page
physicalPositions<- Man page
physicalPositions<-,MareyMap-method Man page
physicalPositions<--methods Man page
plot,MareyMap,Interpolation-method Man page
plot,MareyMap,MMLoess-method Man page
plot,MareyMap,MMSlidingWindow-method Man page
plot,MareyMap,MMSpline3-method Man page
plot,MareyMap,missing-method Man page
plotMarkers Man page
plotMarkers,MareyMap-method Man page
plotMarkers-methods Man page
plotModel Man page
plotModel,Interpolation-method Man page
plotModel,MMLoess-method Man page
plotModel,MMSlidingWindow-method Man page
plotModel,MMSpline3-method Man page
plotModel-methods Man page
plotModels Man page
plotModels,MareyMap-method Man page
plotModels-methods Man page
plotRate Man page
plotRate,Interpolation-method Man page
plotRate,MMLoess-method Man page
plotRate,MMSlidingWindow-method Man page
plotRate,MMSpline3-method Man page
plotRate-methods Man page
plotRates Man page
plotRates,MareyMap-method Man page
plotRates-methods Man page
query Man page
query,Interpolation,integer-method Man page
query,Interpolation,numeric-method Man page
query,MMLoess,numeric-method Man page
query,MMSlidingWindow,numeric-method Man page
query,MMSpline3,numeric-method Man page
query,MareyMap,numeric-method Man page
query-methods Man page
rates Man page
rates,Interpolation-method Man page
rates-methods Man page
rates<- Man page
rates<-,Interpolation-method Man page
rates<--methods Man page
registerInterpolationMethod Man page
registerInterpolationMethod,character,character-method Man page
registerInterpolationMethod-methods Man page
removeMarker Man page
removeMarker,MareyMap,integer-method Man page
removeMarker-methods Man page
setName Man page
setName,MapSet-method Man page
setName,MareyMap-method Man page Man page
setName-methods Man page
setName<- Man page
setName<-,MapSet,character-method Man page
setName<-,MareyMap,ANY-method Man page
setName<--methods Man page
setNames Man page
setNames,MapCollection-method Man page
setNames-methods Man page
shift Man page
shift,MMSlidingWindow-method Man page
shift<- Man page
shift<-,MMSlidingWindow-method Man page
size Man page
size,MMSlidingWindow-method Man page
size<- Man page
size<-,MMSlidingWindow-method Man page
span Man page
span,MMLoess-method Man page
span<- Man page
span<-,MMLoess-method Man page
spar Man page
spar,MMSpline3-method Man page
spar<- Man page
spar<-,MMSpline3,numeric-method Man page
startMareyMapGUI Man page
startMareyMapGUI,missing-method Man page
startMareyMapGUI-methods Man page
textFile Man page
textFile,MapCollection,character-method Man page
textFile,MapSet,character-method Man page
textFile,MareyMap,character-method Man page
textFile-methods Man page
threshold Man page
threshold,MMSlidingWindow-method Man page
threshold<- Man page
threshold<-,MMSlidingWindow-method Man page
type Man page
type,MMSpline3-method Man page
type<- Man page
type<-,MMSpline3,character-method Man page
userParam Man page
userParam,Interpolation-method Man page
userParam,MMLoess-method Man page
userParam,MMSlidingWindow-method Man page
userParam,MMSpline3-method Man page
userParam-methods Man page
validPositions Man page
validPositions,MareyMap-method Man page
validPositions-methods Man page
visible Man page
visible,Interpolation-method Man page
visible-methods Man page
visible<- Man page
visible<-,Interpolation-method Man page
visible<--methods Man page

Files

COPYING
inst
inst/stock_delete.gif
inst/gnome-settings.gif
inst/gtk-add.gif
inst/license.txt
inst/stock_color.gif
inst/stock_save.gif
inst/stock_help-agent.gif
inst/about.txt
inst/stock_show-all.gif
inst/doc
inst/doc/vignette.Rnw
inst/doc/vignette.pdf
NAMESPACE
data
data/Arabidopsis_thaliana.rda
data/Homo_sapiens_female.rda
data/Caenorhabditis_elegans.rda
data/Homo_sapiens_male.rda
data/Homo_sapiens_mean.rda
data/Drosophila_melanogaster.rda
R
R/AllClasses.R
R/PlotArea.R
R/Registry.R
R/MarkerInfo.R
R/MareyMap.Methods.R
R/MapSet.Methods.R
R/mmspline3.R
R/MenuBar.R
R/startMareyMapGUI.R
R/InterpolationParam.Methods.R
R/mmloess.R
R/InterpolationList.R
R/mmslidingwindow.R
R/Interpolation.Methods.R
R/AllGeneric.R
R/MapCollection.Methods.R
R/LocalRateQuery.R
R/MapList.R
vignettes
vignettes/vignette.Rnw
vignettes/vignette-concordance.tex
vignettes/severalqueries.png
vignettes/stock_save.png
vignettes/listmethods.png
vignettes/loessmethod.png
vignettes/gnome-settings.png
vignettes/opendata.png
vignettes/test_query.txt
vignettes/slidingwindowmethod.png
vignettes/gtk-add.png
vignettes/splinemethod.png
vignettes/stock_delete.png
vignettes/start.png
vignettes/interactivequery.png
vignettes/stock_show-all.png
MD5
build
build/vignette.rds
DESCRIPTION
man
man/registerInterpolationMethod-methods.Rd
man/paramDefault-methods.Rd
man/paramMax-methods.Rd
man/rates-methods.Rd
man/paramName-methods.Rd
man/interpolation-methods.Rd
man/plotModel-methods.Rd
man/mapName-methods.Rd
man/persistent-methods.Rd
man/InterpolationParam-class.Rd
man/plotRates-methods.Rd
man/MareyMap-class.Rd
man/plotMarkers-methods.Rd
man/createOrder-methods.Rd
man/Homo_sapiens.Rd
man/Drosophila_melanogaster.Rd
man/argList-methods.Rd
man/plotModels-methods.Rd
man/speciesName-methods.Rd
man/MapCollection-class.Rd
man/speciesNames-methods.Rd
man/markerValidity-methods.Rd
man/mapNames-methods.Rd
man/SpeciesMaps-methods.Rd
man/Interpolation-class.Rd
man/validPositions-methods.Rd
man/interpolate-methods.Rd
man/physicalPositions-methods.Rd
man/paramDesc-methods.Rd
man/InterpolationParam-methods.Rd
man/Arabidopsis_thaliana.Rd
man/getInterList-methods.Rd
man/paramMin-methods.Rd
man/MMSlidingWindow-class.Rd
man/SpeciesMaps-class.Rd
man/query-methods.Rd
man/Caenorhabditis_elegans.Rd
man/startMareyMapGUI-methods.Rd
man/markerNames-methods.Rd
man/paramValues-methods.Rd
man/visible-methods.Rd
man/MareyMap-methods.Rd
man/interpolations-methods.Rd
man/userParam-methods.Rd
man/MapCollection-methods.Rd
man/name-Methods.Rd
man/color-methods.Rd
man/plotRate-methods.Rd
man/textFile-methods.Rd
man/geneticDistances-methods.Rd
man/paramType-methods.Rd
man/removeMarker-methods.Rd
man/MMSpline3-class.Rd
man/MMLoess-class.Rd
man/paramFun-methods.Rd
MareyMap documentation built on May 19, 2017, 10:31 a.m.