multipleFamilyPValue: probability of sharing of rare variants in a subset of...

In RVS: Computes estimates of the probability of related individuals sharing a rare variant

Description

Computing probability of sharing of rare variants in a subset of families where rare variants are seen based on precomputed family-specific rare variant sharing probabilities.

Usage

multipleFamilyPValue(sharingProbs, observedSharing, minPValue = 0)

Arguments

sharingProbs	named vector of sharing probabilties, where names correspond to famid value of pedigree
observedSharing	boolean vector describing if all affected subjects in the family share the variant (TRUE if all share)
minPValue	the minimum p-value threshold, once the true p-value is determined to be less than this, the computation stops and minPValue is returned - this prevents extremely long computations for extremely small p-values

Details

All the subsets of families of size equal or inferior to the length of not are created, and the joint probability of each such subset not sharing a rare variant and the remaining families sharing a rare variant is obtained as the product of the family-specific rare variant sharing probabilities or its complement. The function then sums the pattern probabilities inferior or equal to the probability of the observed pattern of the not families not sharing a rare variant and the remaining families sharing a rare variant.

Value

P-value of the exact rare variant sharing test requiring sharing by all affected subjects

References

Bureau, A., Younkin, S., Parker, M.M., Bailey-Wilson, J.E., Marazita, M.L., Murray, J.C., Mangold, E., Albacha-Hejazi, H., Beaty, T.H. and Ruczinski, I. (2014) Inferring rare disease risk variants based on exact probabilities of sharing by multiple affected relatives. Bioinformatics, 30(15): 2189-96, doi:10.1093/bioinformatics/btu198.

Examples

data(samplePedigrees)
probs <- sapply(samplePedigrees, RVsharing)
notSharedFams <- c(15159, 15053, 15157)
famids <- sapply(samplePedigrees, function(p) p$famid[1])
shared <- !famids %in% notSharedFams
names(shared) <- names(probs)
multipleFamilyPValue(probs, shared)

RVS documentation built on Nov. 8, 2020, 6:57 p.m.