score.pedigree: Take the encoded information about the pedigrees and...

In KinformR: Relationship-Informed Pedigree and Variant Scoring

Take the encoded information about the pedigrees and calculate penetrance.

Description

Determine a value score of families by comparing their relationship structure. More distant relationships between affecteds (e.g. affected cousins) is more valuable that close relationships (e.g. affected siblings) as there is less IBD and therefore a smaller search space.

Usage

score.pedigree(h)

Arguments

h	A data frame containing the encoded pedigree information

Details

Simplifying assumptions:

• Autosomal dominant

• No ambiguous statuses

• No more than two sequential generations of unknown carrier status (non-obligate carrier vs. non-carrier). Generalized support of arbitrary tree structures gets a lot more complicated, especially for the likelihood function.

• Exclude big giant trees of unaffecteds - related to above. Will slightly bias the result toward higher penetrance.

• Exclude subjects younger than age of onset

Value

A data frame containing the theoretical scoring of the power of a family assuming you were able to collect everyone on the simplified pedigree, as well as a current scoreing, examining only those for whom you currently have DNA.

Examples

example.pedigree.file <-system.file('extdata/example_pedigree_encoding.tsv',
package = 'KinformR')
example.pedigree.df <- read.pedigree(example.pedigree.file)
penetrance.df <- score.pedigree(example.pedigree.df)

KinformR documentation built on Feb. 17, 2026, 5:07 p.m.