Description Usage Arguments Details Value References Examples
Given k relatives of the proband, among which m are affected, probFamilial calculates the probability that the pedigree is segregating familial disease as opposed to simply having m sporadic cases.
1 | probFamilial(m, k, pf, pr, priorF, r = 0)
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m |
Number of affected relatives of the proband. |
k |
Number of relatives of the proband with known affection status. |
pf |
Probability of relative being affected with familial disease. |
pr |
Probability of relative being affected with sporadic disease. |
priorF |
Prior probability that a pedigree is segregating familial disease. |
r |
Number of sporadic cases allowed when calculating probability that all cases are familial. |
pf can be understood as a combination of penetrance and relatedness. For example, considering 1st degree relatives and a fully penetrant dominant mutation, pf=0.5 since a full sibling of the proband has 0.5 prob of inheriting the same mutation, a child of the proband has 0.5 prob of receiving the mutation, and a parent of the proband has 0.5 prob of being the one who transmitted the mutation. For general pedigrees containing a mix of relationships, pf can be understood as the average over all observed relatives to the proband.
For a rare disease, pr is approximately the population lifetime risk.
If parameter r equals 0, the returned value allFamilial is the probability that all m cases have the familial form of disease. Otherwise allFamilial is the probability that at least (m-r) of the m cases have the familial form.
mprob Probability of m affected relatives in a pedigree segregating familial disease (equation 2 in Dudbridge et al).
rprob Probability of m affected relatives in a pedigree with only sporadic disease (calculated as a binomial probability).
probFamilial Posterior probability that the pedigree is segregating familial disease.
allFamilial Posterior probability that all the cases in a pedigree are familial, except for up to r sporadic cases.
Dudbridge F, Brown SJ, Ward L, Wilson SG, Walsh JP. How many cases of disease in a pedigree imply familial disease? Submitted.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 | # Familial nonmedullary thyroid cancer, figure 1 in Dudbridge et al.
pf <- 0.0981
pr <- 0.0031
priorF <- 0.013
for(k in 2:8)
print(probFamilial(1,k,pf,pr,priorF)$probFamilial)
for(k in 2:8)
print(probFamilial(2,k,pf,pr,priorF)$probFamilial)
# Colorectal cancer, probabilities that all cases are familial
pf <- 0.2
pr <- 0.05
priorF <- 0.0865
probFamilial(2,8,pf,pr,priorF)$allFamilial
# [1] 0.6944444
probFamilial(8,8,pf,pr,priorF)$allFamilial
# [1] 0.232568
# Allowing up to one sporadic case in the pedigree
probFamilial(2,8,pf,pr,priorF,r=1)$allFamilial
# [1] 0.9722222
probFamilial(8,8,pf,pr,priorF,r=1)$allFamilial
# [1] 0.6046769
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