peelingRC: Peeling interface in R.

In wwylab/LFSPRO: TP53 germline mutation carrier estimation and cancer risk predictions

Peeling interface in R.

Description

peelingRC is based on Elston-Stewart algorithm and it is a low level function has been integrated in lfsproC, lfsproC.cs and lfsproC.mpc. We implemented the function in C++ to improve computation so peelingRC linked the peeling algorithm in C++ version to R.

Usage

peelingRC(allef, LIK, ped, counselee.id, nloci = 1, mRate = 0)

Arguments

allef	List. Allele frequency for each locus/gene. If there is only one gene and two alleles in the gene (allele frequency is 0.1 and 0.9), allef = list(c(0.1,0.9)), If there are two genes,two alleles (allele frequency is 0.1 and 0.9) for gene 1 and three alleles (allele frequncy is 0.2, 0.2 and 0.6) for gene 2. allef = list(c(0.1,0.9),c(0.2,0.2,0.6))
LIK	Matrix, likelihood, Pr(D|G), for three genotypes for all individuals in the family. D: healthy status. G: genotype.
ped	Pedigree structure. A data frame with four varaibles: ID (individual id), Gender (sex, 0: female, 1: male), FatherID (father id) and MotherID (mother id).
counselee.id	Individual id for the counselee. If you want to estimate multiple samples at the same time, just set counselee.id as a vector of IDs for all the samples.
nloci	Number of loci/genes in the model.
mRate	Mutation rate.

Details

One family a time.

Value

The posterior probability (Pr(G|D)) for each counselee

Author(s)

Gang Peng

References

Elston, R. C., Stewart, J. (1971) A general model for the genetic analysis of pedigree data. Hum Hered., 21, 523-542.

See Also

lfsproC

wwylab/LFSPRO documentation built on Feb. 1, 2023, 1:05 a.m.