ibd1.parental: Estimates for a pair of non-inbred individuals the...

In mut: Pairwise Likelihood Ratios

Description

Assume IBD is 1 for a pair of non-inbred individuals. The function estimates the probabilities of the four possible combinations of parental origin: (i) paternal-paternal, (ii) paternal-maternal, (iii) maternal-paternal and (iv) maternal-maternal.

Usage

ibd1.parental(x, id.pair, Nsim, cM = 10000, verbose = F, ...)
uniformMap(Mb = NULL, cM = NULL, M = NULL, cm.per.mb = 1, 
	        chromosome = 1) 

Arguments

x	A pedigree in the form of a linkdat object.
id.pair	Integer vector of length 2 giving the pair of individuals.
Nsim	Integer. Number of simulations.
cM	NULL, or a non-negative number: The distance in centiMorgan between the two loci.
verbose	logical
...	Further arguments to be passed on to IBDsim.
Mb	Double
M	Double
cm.per.mb	Double
chromosome	integer

Details

This is a wrapper for IBDsim.

Value

alpha.sample	Each column gives the four alpha values.
alpha.hat	Estimates of alpha.

Author(s)

Magnus Dehli Vigeland and Thore Egeland

See Also

IBDsim.

Examples

library(IBDsim)
x = doubleFirstCousins()
ids = c(9,10)
ibd1.parental(x, ids, 10)$alpha.hat
x = swapSex(x,3)
ibd1.parental(x, ids, 10)$alpha.hat

mut documentation built on May 2, 2019, 11:10 a.m.