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The kinship2 Package

Initially a set of functions to view pedigrees while developing models that use kinship matrices, the functions were useful enough to put into a package of its own, an S3 class for pedigrees, kinship function that calculates the kinship matrix from a pedigree object, and the pedigree plotting routines that adhere to many of the standards for genetics counselors.

The pedigree() Function

pedigree() is a function that creates an S3 class of either one pedigree of a pedigreeList (list of pedigrees), depending on whether the family id is given. The core of the pedigree object is built from having a row per person, linked by the father id and mother id. Other relationships can be specified, and affection status can be a matrix of multiple categories.

The plot.pedigree() Method

plot.pedigree() is a method for pedigree a object that plots as a “family tree”, with relatives of the same generation on the same row, and affection statuses divided over the plot symbol for each person.

The kinship() Funtion

kinship() is a function that creates the kinship matrix from a pedigree object. It is coded for dyplotype organisms, handling all relationships that can be specified for the pedigree object, including inbreeding, monozygotic twins, etc. A recent addition is handling the kinship matrix for the X and Y chromosomes.

Other Notable Functions

• pedigree.shrink() will shrink a pedigree to a given size, keeping the most informative individuals for a single affection variable.

• fixParents() will add parents for children who have a mother or dad listed that is not already included. It will also fix the sex status for the parent if it is mis-specified.

• legendPlot() is a variation on plot.pedigree, which has an informative legend at the bottom with the ability to put labels for the affection statuses and coloring scheme.

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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