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paramlink  

Parametric Linkage and Other Pedigree Analysis in R
View on CRAN: Click here


Download and install paramlink package within the R console
Install from CRAN:
install.packages("paramlink")

Install from Github:
library("remotes")
install_github("cran/paramlink")

Install by package version:
library("remotes")
install_version("paramlink", "1.1-5")



Attach the package and use:
library("paramlink")
Maintained by
Magnus Dehli Vigeland
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2011-03-20
Latest Update: 2022-04-15
Description:
NOTE: 'PARAMLINK' HAS BEEN SUPERSEDED BY THE 'PED SUITE' PACKAGES (). 'PARAMLINK' IS MAINTAINED ONLY FOR LEGACY PURPOSES AND SHOULD NOT BE USED IN NEW PROJECTS. A suite of tools for analysing pedigrees with marker data, including parametric linkage analysis, forensic computations, relatedness analysis and marker simulations. The core of the package is an implementation of the Elston-Stewart algorithm for pedigree likelihoods, extended to allow mutations as well as complex inbreeding. Features for linkage analysis include singlepoint LOD scores, power analysis, and multipoint analysis (the latter through a wrapper to the 'MERLIN' software). Forensic applications include exclusion probabilities, genotype distributions and conditional simulations. Data from the 'Familias' software can be imported and analysed in 'paramlink'. Finally, 'paramlink' offers many utility functions for creating, manipulating and plotting pedigrees with or without marker data (the actual plotting is done by the 'kinship2' package).
How to cite:
Magnus Dehli Vigeland (2011). paramlink: Parametric Linkage and Other Pedigree Analysis in R. R package version 1.1-5, https://cran.r-project.org/web/packages/paramlink
Previous versions and publish date:
0.2-1 (2011-03-20 20:39), 0.3-1 (2011-10-15 21:53), 0.6-1 (2012-02-01 21:07), 0.7-0 (2012-08-10 13:54), 0.8-0 (2012-12-12 17:25), 0.8-3 (2013-04-03 01:29), 0.9-1 (2013-04-15 08:11), 0.9-6 (2014-04-01 11:52), 0.9-7 (2015-07-03 12:51), 0.9-8 (2016-04-28 00:28), 0.9-9 (2016-10-17 00:38), 1.1-0 (2017-03-13 13:18), 1.1-1 (2017-08-14 17:08), 1.1-2 (2018-01-05 17:06), 1.1-4 (2022-02-21 17:00)
Other packages that cited paramlink R package
View paramlink citation profile
Other R packages that paramlink depends, imports, suggests or enhances
Functions, R codes and Examples using the paramlink R package
Some associated functions: Familias2linkdat . IBDestimate . IBDtriangle . LR . Xped . allGenotypes . as.data.frame.linkdat . as.matrix.linkdat . dominant . examineKinships . exclusionPower . hasCA . is.linkdat . likelihood . linkage.power . linkageSim . linkdat . linkres . lod . lod.peaks . markerSim . markers . mendelianCheck . mergePed . merlin . oneMarkerDistribution . paramlink-package . pedCreate . pedModify . pedParts . pedigreeLoops . plot.linkdat . plotPedList . randomPed . readDatfile . relatednessCoeff . relationLR . setAvailable . setModel . setPlotLabels . showInTriangle . simpleSim . toyped . transferMarkerdata . twoMarkerDistribution . twoloops . 
Some associated R codes: IBDest_getAlleleData.R . IBDestimate.R . IBDtriangle.R . LR.R . SNPsim.R . all.equal.linkdat.R . allGenotypes.R . as.data.frame.linkdat.R . as.matrix.linkdat.R . datasets.R . depreciated.R . examineKinships.R . exclusionPower.R . familias2linkdat.R . is.linkdat.R . likelihood.R . likelihoodSNP.R . likelihood_LINKAGE.R . linkage.power.R . linkageSim.R . linkdat.R . linkres.R . lod.R . loops.R . markerSim.R . markers.R . mendelianCheck.R . mergePed.R . merlin.R . oneMarkerDistribution.R . paramlink.R . pedCreate.R . pedModify.R . pedParts.R . plot.linkdat.R . plotPedList.R . randomPed.R . readDatfile.R . relatednessCoeff.R . relationLR.R . setModel.R . setPlotLabels.R . transferMarkerdata.R . twoMarkerDistribution.R . utils.R . zzz.R .  Full paramlink package functions and examples
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