Package: MareyMap 1.3.10

Aurélie Siberchicot

MareyMap: Estimation of Meiotic Recombination Rates Using Marey Maps

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

Authors:Gabriel Marais [aut], Clément Rezvoy [aut], Delphine Charif [aut], Laurent Gueguen [aut], Aurélie Siberchicot [ctb, cre]

MareyMap_1.3.10.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
MareyMap/json (API)

# Install 'MareyMap' in R:

install.packages('MareyMap', repos = c('https://lbbe-software.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/lbbe-software/mareymap/issues

Datasets:

Arabidopsis_thaliana - The marey map for the species Arabidopsis thaliana
Caenorhabditis_elegans - The marey map for the species Caenorhabditis_elegans
Drosophila_melanogaster - The marey map for the species Drosophila melanogaster
Homo_sapiens_female - The marey map for the species Homo sapiens
Homo_sapiens_male - The marey map for the species Homo sapiens
Homo_sapiens_mean - The marey map for the species Homo sapiens

On CRAN:

5.57 score 2 stars 37 scripts 296 downloads 17 mentions 87 exports 0 dependencies

Last updated from:b7425e5cd6. Checks:9 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	OK	176
source / vignettes	OK	232
linux-release-x86_64	OK	146
macos-release-arm64	OK	82
macos-oldrel-arm64	OK	115
windows-devel	OK	74
windows-release	OK	87
windows-oldrel	OK	93
wasm-release	OK	88

Exports:argList coerce color color<-createOrder degree degree<-df df<-gcv gcv<-geneticDistances geneticDistances<-getInterList interpolate interpolation interpolation<-InterpolationParam interpolations interpolations<-MapCollection mapName mapName<-mapNames MapSet MareyMap markerNames markerNames<-markerValidity markerValidity<-MMLoess MMSlidingWindow MMSpline3 name name<-paramDefault paramDefault<-paramDesc paramDesc<-paramFun paramFun<-paramMax paramMax<-paramMin paramMin<-paramName paramName<-paramType paramType<-paramValues paramValues<-persistent persistent<-physicalPositions physicalPositions<-plot plotMarkers plotModel plotModels plotRate plotRates query rates rates<-registerInterpolationMethod removeMarker setName setName<-setNames shift shift<-size size<-span span<-spar spar<-startMareyMapGUI textFile threshold threshold<-type type<-userParam validPositions visible visible<-

Dependencies:

Using the MareyMap package

Rendered fromvignette.Rnwusingutils::Sweave

Last update: 2022-12-12
Started: 2016-01-05

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
The marey map for the species Arabidopsis thaliana	Arabidopsis_thaliana
Methods for function argList in package 'MareyMap'	argList argList-methods
The marey map for the species Caenorhabditis_elegans	Caenorhabditis_elegans
Accessors for slot color in package 'MareyMap'	color color-methods color<- color<--methods
createOrder	createOrder createOrder-methods
The marey map for the species Drosophila melanogaster	Drosophila_melanogaster
Accessors for slot geneticDistances	geneticDistances geneticDistances-methods geneticDistances<- geneticDistances<--methods
returns a list of interpolation methods.	getInterList getInterList,missing-method getInterList-methods
The marey map for the species Homo sapiens (female, male and mean of the two)	Homo_sapiens_female Homo_sapiens_male Homo_sapiens_mean
interpolate	interpolate interpolate-methods
Class "Interpolation"	argList,Interpolation-method color,Interpolation-method color<-,Interpolation-method interpolate,Interpolation,MareyMap-method Interpolation Interpolation-class name,Interpolation-method name<-,Interpolation-method persistent,Interpolation-method persistent<-,Interpolation-method plot,MareyMap,Interpolation-method plotModel,Interpolation-method plotRate,Interpolation-method query,Interpolation,integer-method query,Interpolation,numeric-method rates,Interpolation-method rates<-,Interpolation-method userParam,Interpolation-method visible,Interpolation-method visible<-,Interpolation-method
set or returns an interpolation.	interpolation interpolation-methods interpolation<- interpolation<--methods
Class "InterpolationParam"	InterpolationParam InterpolationParam-class paramDefault,InterpolationParam-method paramDefault<-,InterpolationParam-method paramDesc,InterpolationParam-method paramDesc<-,InterpolationParam,character-method paramFun,InterpolationParam-method paramFun<-,InterpolationParam,character-method paramMax,InterpolationParam-method paramMax<-,InterpolationParam-method paramMin,InterpolationParam-method paramMin<-,InterpolationParam-method paramName,InterpolationParam-method paramName<-,InterpolationParam,character-method paramType,InterpolationParam-method paramType<-,InterpolationParam,character-method paramValues,InterpolationParam-method paramValues<-,InterpolationParam,vector-method
Methods for Function InterpolationParam in Package 'MareyMap'	InterpolationParam,missing-method InterpolationParam-methods
accessors for slot interpolations	interpolations interpolations-methods interpolations<- interpolations<--methods
Class "MapCollection"	$,MapCollection-method +,MapCollection,MapCollection-method +,MapCollection,MapSet-method +,MapCollection,MareyMap-method -,MapCollection,character-method coerce,MapCollection,data.frame-method length,MapCollection-method MapCollection MapCollection,missing-method MapCollection-class setNames,MapCollection-method textFile,MapCollection,character-method [,MapCollection-method [[,MapCollection-method [[<-,MapCollection,ANY,ANY,MapSet-method [[<-,MapCollection,ANY,ANY,MareyMap-method
Constructor for class MapCollection	MapCollection-methods
accessors for the slot mapName	mapName mapName-methods mapName<- mapName<--methods
mapNames	mapNames mapNames-methods
Class "MapSet"	$,MapSet-method +,MapSet,MareyMap-method -,MapSet,character-method coerce,MapSet,data.frame-method length,MapSet-method mapNames,MapSet-method MapSet MapSet-class setName,MapSet-method setName<-,MapSet,character-method textFile,MapSet,character-method [,MapSet-method [[,MapSet-method [[<-,MapSet,ANY,ANY,MareyMap-method
Constructor for the class MapSet.	MapSet,character-method MapSet-methods
Class "MareyMap"	+,MareyMap,Interpolation-method coerce,data.frame,MareyMap-method coerce,MareyMap,data.frame-method coerce,MareyMap,NULL-method geneticDistances,MareyMap-method geneticDistances<-,MareyMap-method interpolation,MareyMap,character-method interpolation<-,MareyMap,character,Interpolation-method interpolations,MareyMap-method interpolations<-,MareyMap-method mapName,MareyMap-method mapName<-,MareyMap-method MareyMap MareyMap,data.frame,ANY,ANY,ANY-method MareyMap-class markerNames,MareyMap-method markerNames<-,MareyMap-method markerValidity,MareyMap-method markerValidity<-,MareyMap-method physicalPositions,MareyMap-method physicalPositions<-,MareyMap-method plot,MareyMap,missing-method plotMarkers,MareyMap-method plotModels,MareyMap-method plotRates,MareyMap-method query,MareyMap,numeric-method removeMarker,MareyMap,integer-method setName,MareyMap-method setName<-,MareyMap,ANY-method textFile,MareyMap,character-method validPositions,MareyMap-method [,MareyMap-method [[,MareyMap-method [[<-,MareyMap,ANY,ANY,ANY-method [[<-,MareyMap-method
Constructor for object of the class MareyMap.	MareyMap,missing,missing,missing,missing-method MareyMap-methods
Accessors for the class markerNames.	markerNames markerNames-methods markerNames<- markerNames<--methods
accessors for slot markerValidity	markerValidity markerValidity-methods markerValidity<- markerValidity<--methods
Class "MMLoess". Interpolation method plug-in for MareyMap	createOrder,MMLoess-method degree degree,MMLoess-method degree<- degree<-,MMLoess-method interpolate,MMLoess,MareyMap-method MMLoess MMLoess,missing-method MMLoess-class MMLoess-methods plot,MareyMap,MMLoess-method plotModel,MMLoess-method plotRate,MMLoess-method query,MMLoess,numeric-method span span,MMLoess-method span<- span<-,MMLoess-method userParam,MMLoess-method
Class "MMSlidingWindow" Interpolation method plug-in for MareyMap	createOrder,MMSlidingWindow-method interpolate,MMSlidingWindow,MareyMap-method MMSlidingWindow MMSlidingWindow,missing-method MMSlidingWindow-class MMSlidingWindow-methods plot,MareyMap,MMSlidingWindow-method plotModel,MMSlidingWindow-method plotRate,MMSlidingWindow-method query,MMSlidingWindow,numeric-method shift shift,MMSlidingWindow-method shift<- shift<-,MMSlidingWindow-method size size,MMSlidingWindow-method size<- size<-,MMSlidingWindow-method threshold threshold,MMSlidingWindow-method threshold<- threshold<-,MMSlidingWindow-method userParam,MMSlidingWindow-method
Class "MMSpline3" Interpolation using cubic splines	createOrder,MMSpline3-method df df,MMSpline3-method df<- df<-,MMSpline3,numeric-method gcv gcv,MMSpline3-method gcv<- gcv<-,MMSpline3,logical-method interpolate,MMSpline3,MareyMap-method MMSpline3 MMSpline3,missing-method MMSpline3-class MMSpline3-methods plot,MareyMap,MMSpline3-method plotModel,MMSpline3-method plotRate,MMSpline3-method query,MMSpline3,numeric-method spar spar,MMSpline3-method spar<- spar<-,MMSpline3,numeric-method type type,MMSpline3-method type<- type<-,MMSpline3,character-method userParam,MMSpline3-method
Accessor for slot name.	name name-methods name<- name<--methods
Accessors for slot paramDefault	paramDefault paramDefault-methods paramDefault<- paramDefault<--methods
Accessors for the slot paramDesc	paramDesc paramDesc-methods paramDesc<- paramDesc<--methods
accessors for the slot paramFun	paramFun paramFun-methods paramFun<- paramFun<--methods
Accessors for the slot paramMax.	paramMax paramMax-methods paramMax<- paramMax<--methods
Accessors for slot paramMin.	paramMin paramMin-methods paramMin<- paramMin<--methods
Accessors for the slot paramName.	paramName paramName-methods paramName<- paramName<--methods
Accessors for the slot paramType.	paramType paramType-methods paramType<- paramType<--methods
Accessor for the slot paramValues.	paramValues paramValues-methods paramValues<- paramValues<--methods
Accessors for the slot persistent.	persistent persistent-methods persistent<- persistent<--methods
Accessors for the slot physicalPositions	physicalPositions physicalPositions-methods physicalPositions<- physicalPositions<--methods
plotMarkers	plotMarkers plotMarkers-methods
plotModel	plotModel plotModel-methods
plotModels	plotModels plotModels-methods
plotRate	plotRate plotRate-methods
plotRates	plotRates plotRates-methods
Methods for Function query	query query-methods
Accessors for the slot rates	rates rates-methods rates<- rates<--methods
registerInterpolationMethods	registerInterpolationMethod registerInterpolationMethod,character,character-method registerInterpolationMethod-methods
removeMarker	removeMarker removeMarker-methods
Accessors for the slot setName.	setName setName-methods setName<- setName<--methods
setNames	setNames setNames-methods
MareyMapGUI launcher	startMareyMapGUI startMareyMapGUI,missing-method startMareyMapGUI-methods
textFile	textFile textFile-methods
userParam	userParam userParam-methods
validPositions	validPositions validPositions-methods
Accessors for the slot visible	visible visible-methods visible<- visible<--methods