Ratio of excess kinship among descendants over mean kinship among founders

Description

Computes, for each pair of final descendants in the pedigree structure contained in the pedigree object, the ratio of the difference between the inferred and expected kinship coefficient for the pair over the mean kinship among founders.

Usage

## S4 method for signature 'RVsharingProb'
ComputeKinshipPropCoef(obj)

Arguments

Details

The ratio for each pair of final descendants is computed using equation (A1) of Bureau et al. Dividing the difference between the inferred and expected kinship coefficient for each pair by this ratio gives a pair-specific estimate of the mean kinship among founders, which can then be averaged over all pairs of final descendants from the same population to obtain a global estimate of the mean kinship among founders.

Value

A symmetric matrix of ratios for all pair of final descendants in the pedigree structure contained in the pedigree object.

Author(s)

Alexandre Bureau <alexandre.bureau@msp.ulaval.ca>

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.

See Also

pedigree

Examples

data(ped.list)
plot(ped.list[[1]])
obj = RVsharing(ped.list[[1]])
ComputeKinshipPropCoef(obj)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(RVsharing)

Welcome to RVsharing version 1.6.0

> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/RVsharing/compute.kinship.prop.coef.Rd_%03d_medium.png", width=480, height=480)
> ### Name: ComputeKinshipPropCoef-method
> ### Title: Ratio of excess kinship among descendants over mean kinship
> ###   among founders
> ### Aliases: ComputeKinshipPropCoef
> ###   ComputeKinshipPropCoef,RVsharingProb-method
> 
> ### ** Examples
> 
> data(ped.list)
> plot(ped.list[[1]])
> obj = RVsharing(ped.list[[1]])
> ComputeKinshipPropCoef(obj)
       [,1]
[1,] 0.9375
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>