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paramlink (version 0.8-3)

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

0.8-3

License

GPL (>= 2)

Maintainer

Magnus Dehli Vigeland

Last Published

April 2nd, 2013

Functions in paramlink (0.8-3)

twoloops

A consanguineous pedigree
linkdat

linkdat objects
markers

Marker functions
linkage.power

Power of a linkage study
setAvailable

Functions for modifying availability vectors
toyped

Toy pedigree for linkage analysis
randomPed

Random pedigree
simpleSim

Marker simulation
linkdat.utils

linkdat utilities
twoMarkerDistribution

Genotype probability distribution
setModel

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

Power of exclusion
markerSim

Marker simulation
plot.linkdat

Plot pedigrees with genotypes
lod

Two-point LOD score
dominant

Example pedigree for linkage analysis: 23 individuals, 650 SNPs
createPedigree

Create simple pedigrees
likelihood

Pedigree likelihood
Xped

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

linkdat to matrix conversions
modifyPedigree

Modify the pedigree of 'linkdat' objects
oneMarkerDistribution

Genotype probability distribution
SNPsim

Simulate SNP markers
merlin

MERLIN wrapper function
linkres

S3 methods for class 'linkres'.