Genotype probability distribution
Computes the joint genotype distribution of two markers for a specified pedigree member, conditional on existing genotypes and pedigree information.
twoMarkerDistribution(x, id, partialmarker1, partialmarker2, theta, loop_breakers = NULL, eliminate = 99, verbose = TRUE)
x |
A |
id |
The individual in question. |
partialmarker1, partialmarker2 |
Either a single integer indicating the
number of one of |
theta |
A single numeric in the interval [0, 0.5] - the recombination fraction between the two markers. |
loop_breakers |
A numeric containing IDs of individuals to be used as
loop breakers. Relevant only if the pedigree has loops. See
|
eliminate |
A non-negative integer, indicating the number of iterations
in the internal genotype-compatibility algorithm. Positive values can save
time if |
verbose |
A logical. |
A named matrix giving the joint genotype distribution.
Magnus Dehli Vigeland
x = nuclearPed(2)
emptySNP = marker(x, alleles=c('a','b'))
SNP1 = marker(x, 1, c(1,1), 2, c(1,0), alleles=1:2, afreq=c(0.1, 0.9))
twoMarkerDistribution(x, id=2, emptySNP, SNP1, theta=0)
twoMarkerDistribution(x, id=2, emptySNP, SNP1, theta=0.5)
twoMarkerDistribution(x, id=3, emptySNP, SNP1, theta=0.5)
# X-linked example
SNPX_1 = marker(x, 2, c('a','b'), 3, 'b', alleles=c('a','b'), chrom=23)
SNPX_2 = marker(x, 2, c('a','b'), 3, 'b', alleles=c('a','b'), chrom=23)
r1 = twoMarkerDistribution(x, id=4, SNPX_1, SNPX_2, theta=0)
r2 = twoMarkerDistribution(x, id=4, SNPX_1, SNPX_2, theta=0.5)
stopifnot(all(r1==c(.5,0,0,.5)), all(r2==c(.25,.25,.25,.25)))Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.