Dear all,

I'd like to introduce the paramlink package, offering parametric linkage analysis in R, as well as other likelihood-based pedigree analyses. While a rudimentary version of the package has existed for a while, it was never properly introduced to this forum. The present version is a major update with new and improved functions.

Features:
* Singlepoint LOD scores for simple/complex/inbred pedigrees (implementing the Elston-Stewart algorithm). Allows partial genotypes (i.e. with one missing allele) * Multipoint analysis is provided through a wrapper for MERLIN. The wrapper creates all necessary files automatically, and makes it easy to re-run analysis under different models or with subsets of pedigree members/markers. * Power analysis for linkage (implementing the simulation algorithm of SLINK). * Nice pedigree plots produced by importing the kinship2 package. Includes flexible plotting of marker genotypes.
* LOD score plots.
* Reads and writes ped/map/dat/freq/model files in MERLIN format.
* Computation of genotype probability distributions, unconditional or conditional on partial marker data: - For a single marker, the joint genotype distribution of any number of family members. - For a single individual, the joint genotype distribution of two linked markers. * Many utility functions for creating/modifying pedigrees. This is usually quicker than writing pedigree files from scratch in a text editor.

There is a vignette with an introduction to the main features: http://cran.r-project.org/web/packages/paramlink/vignettes/paramlink.pdf

Feedback, bug reports and feature requests are most welcome.

Regards,
Magnus

--
Magnus Dehli Vigeland, PhD
Department of Medical Genetics
University of Oslo
Norway

E-mail: magnu...@medisin.uio.no
Phone: +47 22 11 98 79

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