probAffectedRelative: Probability of a relative being affected with familial...

In DudbridgeLab/familialdisease: Probability calculations for pedigrees segregating a familial form of disease

Description

Given a series of pedigrees of different sizes, each with at least r affected relatives of the proband, probAffectedRelative estimates the probability of a relative being affected with familial disease, where this probability is an average over all observed relationships to probands. This probability can be used at the pf parameter in the probFamilial function.

Usage

probAffectedRelative(m, k, r)

Arguments

m	Vector in which each element corresponds to a pedigree and is the number of affected relatives of the proband.
k	Vector in which element corresponds to a pedigree and is the number of relatives of the proband with known affection status.
r	Minimum number of affected relatives in each pedigree.

Details

Parameter r accounts for ascertainment of pedigrees that are highly likely to segregate familial disease.

Each pedigree contributes to the likelihood the binomial probability of m successes in k trials, conditional on at least r successes. Estimation is then by maximum likelihood.

Value

Probability of a relative being affected with familial disease.

References

Dudbridge F, Brown SJ, Ward L, Wilson SG, Walsh JP. How many cases of disease in a pedigree imply familial disease? Submitted.

Charkes ND (2006) On the Prevalence of Familial Nonmedullary Thyroid Cancer in Multiply Affected Kindreds. Thryoid 16:181-186

Examples

# Familial nonmedullary thyroid cancer, table 2 in Charkes 2006.
m=c(2,2,2,4,2,2,2)
k=c(9,9,10,7,9,14,7)
probAffectedRelative(m,k,2)

DudbridgeLab/familialdisease documentation built on May 8, 2019, 3:42 p.m.