Pedigree package

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This package was started by Jason Stajich to represent data parsed from files for linkage analysis research. The main components are the Pedigree, Individual, Genotype, and Marker objects. The simpler version of this, when individuals are unrelated, is the basis for the PopGen modules, and the pedigree objects are an extension of the PopGen objects.

Contents

Pedigree

A representation of a research study of individuals (see below). This is a general grouping object and the individuals need not all be related (they will be a GROUP rather than a PEDIGREE) but will be stored in the same object. This object extends the Bio::PopGen::Population object.

Person

This object represents an individual in a study who has some phenotypic, genotypic, and relationship information. The Person will have relatives (a collection of Relationship objects), genotypes for given markers, and sometimes phenotype data.

Marker

This is a representation of some sort of genotypic assay to sample a region of the genome which is polymorphic in a set of individuals.

Draw

This is a collection of modules for rendering. This is mostly a perl implementation of rendering pedigrees of an old-C++ program written by Jason Stajich many moons ago (Stajich JE, Haynes C, Pericak-Vance MA, "Pedplot" 1998 Am J Hum Genet suppl, 63:A242).

PedIO

A parser and writer object for building Pedigree objects from data files and serializing the objects back to flat-file text.

The latest code

The latest, and not completely tested, code can be viewed here:

http://code.open-bio.org/svnweb/index.cgi/bioperl/browse/bioperl-pedigree/trunk

You can download it by following the instructions on the main Subversion page. The repository name is bioperl-pedigree.

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