Package: MDSMap 1.3

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 [aut], Christine A. Hackett [aut], Bram Boskamp [cre]

MDSMap_1.3.tar.gz
MDSMap_1.3.zip(r-4.7-any)MDSMap_1.3.zip(r-4.6-any)
MDSMap_1.3.tar.gz(r-4.7-any)MDSMap_1.3.tar.gz(r-4.6-any)
MDSMap_1.3.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION
card.svg |card.png
MDSMap/json (API)

# Install 'MDSMap' in R:

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

On CRAN:

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

3.08 score 1 packages 430 downloads 4 mentions 18 exports 120 dependencies

Last updated from:fa7212744f. Checks:6 OK. Indexed: yes.

Target	Result	Time
linux-devel	OK	175
source / vignettes	OK	239
linux-release	OK	202
windows-devel	OK	149
windows-release	OK	133
wasm-release	OK	176

Exports:calc.maps.pc calc.maps.sphere calc.nnfit calc.nnfit.from.file calc.nnfit.loci calc.nswaps calc.pair.rf.lod convert.polar dmap dmap.check estimate.map get.dist.loci get.nearest.informative invert.map map.to.interval meandist.from.truth recalc.nnfit.from.map sim.bc.rflod.file

Dependencies:backports base64enc bit bit64 boot broom bslib cachem checkmate class cli clipr cluster codetools colorspace cpp11 crayon data.table digest doParallel dplyr e1071 ellipse evaluate farver fastmap fontawesome forcats foreach foreign Formula fs gdata generics ggplot2 glmnet glue gridExtra gtable gtools haven highr Hmisc hms htmlTable htmltools htmlwidgets isoband iterators jomo jquerylib jsonlite knitr labeling lattice lifecycle lme4 magrittr MASS Matrix memoise mice mime minqa mitml nlme nloptr nnet nnls numDeriv ordinal pan pillar pkgconfig plotrix plyr polynom prettyunits princurve progress proxy purrr R6 rappdirs rbibutils RColorBrewer Rcpp RcppEigen Rdpack readr reformulas reshape rgl rlang rmarkdown rpart rstudioapi S7 sass scales shape smacof stringi stringr survival tibble tidyr tidyselect tinytex tzdb ucminf utf8 vctrs viridisLite vroom weights withr wordcloud xfun yaml

MDSMap: High Density Linkage Maps using Multi-Dimensional Scaling

Rendered fromMDSMap.pdf.asisusingR.rsp::asis

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

Help page	Topics
High density Genetic Linkage Mapping using Multidimensional Scaling	MDSMap-package
Estimate marker positions using Principal Curves	calc.maps.pc
Estimate marker positions using spherically constrained weighted MDS	calc.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

Package: MDSMap 1.3

MDSMap: High Density Genetic Linkage Mapping using Multidimensional Scaling

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Help Manual

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