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paramlink

The paramlink package has been superseded by the ped suite. In particular, the main features of paramlink can now be found in the following packages:

  • pedtools: Basic handling of pedigrees and marker data
  • paramlink2: Parametric linkage analysis
  • forrel: Forensic applications
  • ribd: Relatedness coefficients and IBD triangle

Note that paramlink is not compatible with the ped suite. It is maintained only for legacy purposes and should not be used in new projects.

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Install

install.packages('paramlink')

Monthly Downloads

335

Version

1.1-5

License

GPL (>= 2)

Issues

0

Pull Requests

0

Stars

1

Forks

0

Maintainer

Magnus Vigeland

Last Published

April 15th, 2022

Functions in paramlink (1.1-5)

is.linkdat

Is an object a linkdat object?
lod

Two-point LOD score
lod.peaks

LOD score peaks
likelihood

Pedigree likelihood
oneMarkerDistribution

Genotype probability distribution
markers

Marker functions
merlin

MERLIN wrappers
markerSim

Marker simulation
linkageSim

Simulate markers linked to a disease locus.
linkage.power

Power of a linkage study
pedigreeLoops

Pedigree loops
plot.linkdat

Plot pedigrees with genotypes
plotPedList

Plot a list of pedigrees.
randomPed

Random pedigree
pedCreate

Create simple pedigrees
paramlink-package

paramlink: Parametric Linkage and Other Pedigree Analysis in R
exclusionPower

Power of exclusion
hasCA

Pairwise common ancestors
LR

Likelihood ratios of pedigree hypotheses
twoMarkerDistribution

Genotype probability distribution
mendelianCheck

Check for Mendelian errors
readDatfile

Read dat file in LINKAGE format
twoloops

A consanguineous pedigree
relatednessCoeff

Relatedness coefficients
mergePed

Merge two pedigrees
transferMarkerdata

Transfer marker data
setAvailable

Functions for modifying availability vectors
relationLR

Relationship Likelihood Ratio
toyped

Toy pedigree for linkage analysis
linkres

S3 methods for class 'linkres'.
pedModify

Modify the pedigree of 'linkdat' objects
linkdat

Linkdat objects
pedParts

Pedigree subsets
setModel

Set, change or display the model parameters for 'linkdat' objects
setPlotLabels

Attach plot labels to a linkdat object
simpleSim

Unconditional marker simulation
showInTriangle

Add points to the IBD triangle
allGenotypes

Genotype combinations
Familias2linkdat

Convert 'Familias' output to linkdat objects
examineKinships

Check pedigree for relationship errors
dominant

Example pedigree for linkage analysis
IBDtriangle

IBD triangle plot
as.data.frame.linkdat

linkdat to data.frame conversion
IBDestimate

Relatedness estimation
Xped

Example pedigree with X-linked disease pattern.
as.matrix.linkdat

linkdat to matrix conversion