View source: R/twoMarkerDistribution.R
twoMarkerDistribution | R Documentation |
Computes the joint genotype distribution of two markers for a specified pedigree member, conditional on known genotypes and the recombination rate between the markers.
twoMarkerDistribution(
x,
id,
marker1 = 1,
marker2 = 2,
rho = NULL,
loopBreakers = NULL,
lumpSpecial = TRUE,
partialmarker1 = NULL,
partialmarker2 = NULL,
verbose = TRUE
)
x |
A |
id |
A single ID label. |
marker1 , marker2 |
Either |
rho |
A single numeric in the interval |
loopBreakers |
(Only relevant if the pedigree has loops). A vector with
ID labels of individuals to be used as loop breakers. If NULL (default)
loop breakers are selected automatically. See |
lumpSpecial |
A logical, passed on to |
partialmarker1 , partialmarker2 |
(Deprecated) Aliases for |
verbose |
A logical. |
A named matrix giving the joint genotype distribution.
oneMarkerDistribution()
# A sib-pair with two SNPs. The first child is homozygous 1/1.
x = nuclearPed(children = c("bro1", "bro2")) |>
addMarker(bro1 = "1/1", alleles = 1:2, afreq = c(0.5, 0.5)) |>
addMarker(bro1 = "1/1", alleles = 1:2, afreq = c(0.5, 0.5))
plot(x, marker = 1:2)
# Genotype distribution for the brother depends on linkage
twoMarkerDistribution(x, id = "bro2", rho = 0)
twoMarkerDistribution(x, id = "bro2", rho = 0.5)
### Same example on X
y = setChrom(x, marker = 1:2, chrom = "X")
plot(y, marker = 1:2)
twoMarkerDistribution(y, id = "bro2", rho = 0)
twoMarkerDistribution(y, id = "bro2", rho = 0.5)
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