Package: MDSMap 1.1

Bram Boskamp

MDSMap: High Density Genetic Linkage Mapping using Multidimensional Scaling

Estimate genetic linkage maps for markers on a single chromosome (or in a single linkage group) from pairwise recombination fractions or intermarker distances using weighted metric multidimensional scaling. The methods are suitable for autotetraploid as well as diploid populations. Options for assessing the fit to a known map are also provided. Methods are discussed in detail in Preedy and Hackett (2016) <doi:10.1007/s00122-016-2761-8>.

Authors:Katharine F. Preedy <[email protected]>, Christine A. Hackett <[email protected]>

MDSMap_1.1.tar.gz
MDSMap_1.1.tar.gz(r-4.5-noble)MDSMap_1.1.tar.gz(r-4.4-noble)
MDSMap_1.1.tgz(r-4.4-emscripten)MDSMap_1.1.tgz(r-4.3-emscripten)
MDSMap.pdf |MDSMap.html✨
MDSMap/json (API)

# Install 'MDSMap' in R:
install.packages('MDSMap', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

3.26 score 1 packages 15 scripts 242 downloads 4 mentions 18 exports 134 dependencies

Last updated 6 years agofrom:84bd9e176e. Checks:OK: 1 NOTE: 1. Indexed: yes.

TargetResultDate
Doc / VignettesOKOct 10 2024
R-4.5-linuxNOTEOct 10 2024

Exports:calc.maps.pccalc.maps.spherecalc.nnfitcalc.nnfit.from.filecalc.nnfit.locicalc.nswapscalc.pair.rf.lodconvert.polardmapdmap.checkestimate.mapget.dist.lociget.nearest.informativeinvert.mapmap.to.intervalmeandist.from.truthrecalc.nnfit.from.mapsim.bc.rflod.file

Dependencies:abindbackportsbase64encbitbit64bootbroombslibcachemcandisccarcarDatacheckmateclassclicliprclustercodetoolscolorspacecowplotcpp11crayondata.tableDerivdigestdoBydoParalleldplyre1071ellipseevaluatefansifarverfastmapfontawesomeforcatsforeachforeignFormulafsgdatagenericsggplot2glmnetgluegridExtragtablegtoolshavenheplotshighrHmischmshtmlTablehtmltoolshtmlwidgetsisobanditeratorsjomojquerylibjsonliteknitrlabelinglatticelifecyclelme4magrittrMASSMatrixMatrixModelsmemoisemgcvmicemicrobenchmarkmimeminqamitmlmodelrmunsellnlmenloptrnnetnnlsnumDerivordinalpanpbkrtestpillarpkgconfigplotrixplyrpolynomprettyunitsprincurveprogressproxypurrrquantregR6rappdirsRColorBrewerRcppRcppEigenreadrreshaperglrlangrmarkdownrpartrstudioapisassscalesshapesmacofSparseMstringistringrsurvivaltibbletidyrtidyselecttinytextzdbucminfutf8vctrsviridisviridisLitevroomweightswithrwordcloudxfunyaml

MDSMap: High Density Linkage Maps using Multi-Dimensional Scaling

Rendered fromMDSMap.pdf.asisusingR.rsp::asison Oct 10 2024.

Last update: 2017-11-29
Started: 2017-11-29

Readme and manuals

Help Manual

Help pageTopics
High density Genetic Linkage Mapping using Multidimensional ScalingMDSMap-package
Estimate marker positions using Principal Curvescalc.maps.pc
Estimate marker positions using spherically constrained weighted MDScalc.maps.sphere
Calculate the nearest neighbour fit.calc.nnfit
Nearest neighbour fit from estimated map and file of pairwise recombination fractions.calc.nnfit.from.file
Calculates the nearest neighbour fit for an individual marker.calc.nnfit.loci
Calculates the number of swaps required to move from one order to another.calc.nswaps
Create recombination matrix from pairwise data file.calc.pair.rf.lod
Convert Cartesian coordinates from wMDS coordinates to polar coordinates.convert.polar
Calculates pairwise map distances from the recombination fraction.dmap
Reorders a distance map by a new marker order.dmap.check
Load data, estimate a linkage map and plot diagnostics for the fit.estimate.map
Calculates the distance of a marker from some objective "truth".get.dist.loci
For a given marker finds the nearest neighbours with LOD scores > 0.get.nearest.informative
Invert the order of locimap from an estimated map.invert.map
Dataset lgI.txt: pairwise recombination fractions for 143 markers.lgI.txt
Dataset lgV.txt: pairwise recombination fractions for 238 markers.lgV.txt
Map points from MDS final configuration to interval starting at 0.map.to.interval
Calculates mean square distance between marker positions in two different maps.meandist.from.truth
Diagnostic plots for the map estimation using calc.maps.pc with 2 dimensions.plot.pcmap
Diagnostic plots for the map estimation using calc.maps.pc with 3 dimensions.plot.pcmap3d
Produces diagnostic plots for the estimated map using 'calc.maps.sphere'.plot.spheremap
Calculate a nearest neighbour fit from an estimated map object.recalc.nnfit.from.map
Simulate a backcross population from homozygous parents.sim.bc.rflod.file