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, partialmarker1, partialmarker2, rho, loopBreakers = NULL, eliminate = 99, verbose = TRUE )
x |
A |
id |
A single ID label. |
partialmarker1, partialmarker2 |
Either a |
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 |
eliminate |
A non-negative integer, indicating the number of iterations
in the internal algorithm for reducing the genotype space. Positive values
can save time if |
verbose |
A logical. |
A named matrix giving the joint genotype distribution.
Magnus Dehli Vigeland
oneMarkerDistribution()
# A sib-pair pedigree x = nuclearPed(children = c("bro1", "bro2")) # Two SNP markers; first brother homozygous for the `1` allele SNP1 = SNP2 = marker(x, bro1 = "1/1", afreq = c("1" = 0.5, "2" = 0.5)) plot(x, marker = list(SNP1, SNP2)) # Genotype distribution for the brother depends on linkage twoMarkerDistribution(x, id = "bro2", SNP1, SNP2, rho = 0) twoMarkerDistribution(x, id = "bro2", SNP1, SNP2, rho = 0.5) # X-linked chrom(SNP1) = chrom(SNP2) = "X" plot(x, marker = list(SNP1, SNP2)) twoMarkerDistribution(x, id = "bro2", SNP1, SNP2, rho = 0) twoMarkerDistribution(x, id = "bro2", SNP1, SNP2, rho = 0.5)
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