LRpair {BookEKM}R Documentation

LR moments for pairs

Description

SNP markers are assumed. Pairwise relationships are compared. The distribution of LR is computed along with mean and sd, also on log scale.

Usage

LRpair(p1 = c(0.5, 0.5), p2== c(0.5, 0.5), rho = 0.29, ped = NULL, H1 = NULL, H2 = NULL)

Arguments

p1

a numerical vector with allele frequencies for first marker.

p2

a numerical vector with allele frequencies for second marker.

rho

a number in the interval [0,0.5]. Recombination rate

ped

linkdat object

H1

Two integer giving numerator hypothesis of LR

H2

Two integers giving pair denominator hypothesis of LR

Value

table.unique

Unique LR-s and probabilities

table.all

Complete table for all combinations

moments

Summary statistics

Author(s)

Thore Egeland

Examples

require(paramlink)
ped <- nuclearPed( 2, sex = c(1, 2))
res <- LRpair(rho = 0.0, ped = ped, 
              H1 = c( 1, 3), H2 = c(1,2))
stopifnot(res$moments[1,1]==(5/4)^2)

## Not run: 
ped <- nuclearPed(2, sex = c(1, 2))
ped <- addOffspring(ped, mother = 4, noffs = 1)
ped <- addOffspring(ped, father = 5, noffs = 1)
res <- LRpair(rho = 0.0, ped = ped, 
              H1 = c(6, 1), H2 = c(6, 7))
stopifnot(res$moments[1,1] == 73/64)	

## End(Not run)
#
ped <- nuclearPed( 2, sex = c(1, 2))
R=0.5
res <- LRpair(p1 = c( 0.5, 0.5), p2 = c( 0.5, 0.5),
  rho = R, ped = ped, H1 = c( 3,4), H2 = c(1,2))
LR1 = res$moments[1,1]
L1=L2=2

d1 = (2*L1^2+L1*L2+13*L1+2*L2^2+13*L2+33)/64
d2 = (L1-1)*(L2-1)*(4*R+2*(L1+L2+2)*R^2+L1*L2*R^4)/64
LR2 = d1+d2 #LR formula
LR1==LR2

[Package BookEKM version 1.0 Index]