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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.

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Version

Install

install.packages('kinship2')

Monthly Downloads

3,888

Version

1.9.6.1

License

GPL (>= 2)

Maintainer

Last Published

March 24th, 2024

Functions in kinship2 (1.9.6.1)

ibdMatrix

Create an IBD matrix
plot.pedigree.shrink

plot pedigree.shrink object that is a shrunk pedigree object
pedigree.unrelated

Determine set of maximum number of unrelated available subjects from a pedigree
makefamid

Construct a family id from pedigree information
makekinship

Create a sparse kinship matrix
sample.ped

Two example pedigrees
plot.pedigree

plot pedigrees
align.pedigree

Generate plotting information for a pedigree
findUnavailable

Find or trim unavailable subjects in a pedigree
findAvailNonInform

Find subjects from a pedigree who are available and uninformative
bitSize

Calculate pedigree bitsize, defined as 2 * # NonFounders - # Founders
fixParents

Fix details on the parents for children of the pedigree
as.data.frame.pedigree

data.frame from a pedigree object
findAvailAffected

Find a single person to trim from a pedigree whose is available
pedigree.legend

plot a legend for a pedigree
kinship2

The kinship2 package for pedigree data
kindepth

Compute the depth of each subject in a pedigree
minnbreast

Minnesota Breast Cancer Study
kinship

Compute a kinship matrix
autohint

Align a pedigree to print well
pedigree

Create a pedigree or pedigreeList object
pedigree.shrink

Shrink pedigree object
familycheck

Error check for a family classification
testped1

testped1
legendPlot

Legend Pedigree Plot