R packages - Feb 2012 - Major update: paramlink version 0.6-1

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: magnusdv at medisin.uio.no
 Phone: +47 22 11 98 79

_______________________________________________
R-packages mailing list
R-packages at r-project.org
https://stat.ethz.ch/mailman/listinfo/r-packages