Package: MareyMap 1.3.7
Aurélie Siberchicot
MareyMap: Estimation of Meiotic Recombination Rates Using Marey Maps
Local recombination rates are graphically estimated across a genome using Marey maps.
Authors:
MareyMap_1.3.7.tar.gz
MareyMap_1.3.7.zip(r-4.5)MareyMap_1.3.7.zip(r-4.4)MareyMap_1.3.7.zip(r-4.3)
MareyMap_1.3.7.tgz(r-4.4-any)MareyMap_1.3.7.tgz(r-4.3-any)
MareyMap_1.3.7.tar.gz(r-4.5-noble)MareyMap_1.3.7.tar.gz(r-4.4-noble)
MareyMap_1.3.7.tgz(r-4.4-emscripten)MareyMap_1.3.7.tgz(r-4.3-emscripten)
MareyMap.pdf |MareyMap.html✨
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
Last updated 2 months agofrom:e891fe4ff0. Checks:OK: 7. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Aug 18 2024 |
| R-4.5-win | OK | Aug 18 2024 |
| R-4.5-linux | OK | Aug 18 2024 |
| R-4.4-win | OK | Aug 18 2024 |
| R-4.4-mac | OK | Aug 18 2024 |
| R-4.3-win | OK | Aug 18 2024 |
| R-4.3-mac | OK | Aug 18 2024 |
Exports:argListcoercecolorcolor<-createOrderdegreedegree<-dfdf<-gcvgcv<-geneticDistancesgeneticDistances<-getInterListinterpolateinterpolationinterpolation<-InterpolationParaminterpolationsinterpolations<-MapCollectionmapNamemapName<-mapNamesMapSetMareyMapmarkerNamesmarkerNames<-markerValiditymarkerValidity<-MMLoessMMSlidingWindowMMSpline3namename<-paramDefaultparamDefault<-paramDescparamDesc<-paramFunparamFun<-paramMaxparamMax<-paramMinparamMin<-paramNameparamName<-paramTypeparamType<-paramValuesparamValues<-persistentpersistent<-physicalPositionsphysicalPositions<-plotplotMarkersplotModelplotModelsplotRateplotRatesqueryratesrates<-registerInterpolationMethodremoveMarkersetNamesetName<-setNamesshiftshift<-sizesize<-spanspan<-sparspar<-startMareyMapGUItextFilethresholdthreshold<-typetype<-userParamvalidPositionsvisiblevisible<-
Dependencies:
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 |
