exampleKrakow {BookEKM}R Documentation

Krakow homework

Description

For a specific example, detailed in Krakow Sep 1 course, P(M|Hp) and P(M|Hd) are calculated. The conditional likelihoods are done using conditionalLikelihoods and the genotype probabilities, i.e., P(g1,g2) are found using the FamiliasPosterior wrapper mix3Familias. The function indicates how other cases are handled.

Usage

exampleKrakow(p, R, theta, M, c, d)

Arguments

p

Allele frequencies, real vector

R

Mutation rate, real in [0,1]. Default Familias model is used

theta

Kinship coefficient, real in [0,1].

M

Integer vector, subset of 1,2,3,4 for this function.

c

Dropin parameter, real in [0,1]

d

Drop-out. A real vector with two numbers for this function.

Value

lik.p

P(M|Hp)

lik.d

P(M|Hd)

LR

P(M|Hp)/P(M|Hd)

Author(s)

Thore Egeland

References

See Krakow talks.

Examples

#Homework
require(Familias)
require(paramlink)
p <- c(0.01,0.01,0.01,0.97) #allele frequencies
R <- 0 #mutation rate
theta <- 0 #kinship parameter
M <- c(1,2,3) #Mixture
c <- 0.0 #dropin parameter
d <- c(0.0,0.0) #drop-out parameters for the two contributors
exampleKrakow(p, R, theta, M, c,d)

[Package BookEKM version 1.0 Index]