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.