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paramlink (version 0.7-0)

Parametric linkage analysis in R

Description

Parametric linkage analysis and other likelihood-based pedigree analyses based on the Elston-Stewart algorithm, including singlepoint LOD scores, power analysis and computation of marker genotype distributions. Multipoint analysis is provided through a convenient MERLIN wrapper. Includes many utility functions for creating, manipulating and plotting pedigrees, markers and linkage results.

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Version

Install

install.packages('paramlink')

Monthly Downloads

391

Version

0.7-0

License

GPL (>= 2)

Maintainer

Magnus Dehli Vigeland

Last Published

August 10th, 2012

Functions in paramlink (0.7-0)

Xped

Example pedigree with X-linked disease pattern.
SNPsim

Simulate SNP markers
createPedigree

Create simple pedigrees
lod

Two-point LOD score
simpleSim

Marker simulation
setModel

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

Plot pedigrees with genotypes
linkres

S3 methods for class 'linkres'.
twoMarkerDistribution

Genotype probability distribution
linkage.power

Power of a linkage study
markerSim

Simulate SNP markers
oneMarkerDistribution

Genotype probability distribution
randomPed

Random pedigree
merlin

MERLIN wrapper function
twoloops

A consanguineous pedigree
likelihood

Pedigree likelihood
linkdat.utils

linkdat utilities
markers

Marker genotypes for linkdat objects
linkdat

linkdat objects
toyped

Toy pedigree for linkage analysis
setAvailable

Availability vector for 'linkdat' objects
modifyPedigree

Modify the pedigree of 'linkdat' objects
dominant

Example pedigree for linkage analysis: 23 individuals, 650 SNPs