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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