Description Usage Arguments Value Author(s) See Also Examples
View source: R/oneMarkerDistribution.R
Computes the genotype probability distribution of one or several pedigree members, possibly conditional on known genotypes for the marker.
1 2 3 4 5 6 7 8 9 | oneMarkerDistribution(
x,
ids,
partialmarker,
loop_breakers = NULL,
eliminate = 0,
grid.subset = NULL,
verbose = TRUE
)
|
x |
A |
ids |
A numeric with ID labels of one or more pedigree members. |
partialmarker |
Either a |
loop_breakers |
(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 genotype-compatibility algorithm. Positive values can save
time if |
grid.subset |
(Optional; not relevant for most users.) A numeric matrix
describing a subset of all marker genotype combinations for the |
verbose |
A logical. |
A named k
-dimensional array, where k = length(ids)
, with the
joint genotype distribution for the ids
individuals. The probabilities
are conditional on the known genotypes and the allele frequencies of
partialmarker
.
Magnus Dehli Vigeland
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 | # Trivial example giving Hardy-Weinberg probabilities
s = singleton(id = 1)
m = marker(s, alleles = 1:2) # equifrequent SNP
oneMarkerDistribution(s, ids = 1, partialmarker = m)
# Conditioning on a partial genotype
genotype(m, id = 1) = c(1, NA)
oneMarkerDistribution(s, ids = 1, partialmarker = m)
# Genotype distribution for a child of heterozygous parents
trio = nuclearPed(father = "fa", mother = "mo", child = "ch")
m1 = marker(trio, fa = 1:2, mo = 1:2)
oneMarkerDistribution(trio, ids = "ch", partialmarker = m1)
# Joint distribution of the parents, given that the child is heterozygous
m2 = marker(trio, ch = 1:2, alleles = 1:2, afreq = c(0.5, 0.5))
oneMarkerDistribution(trio, ids = c("fa", "mo"), partialmarker = m2)
# A different example: The genotype distribution of an individual (id = 8)
# whose half cousin (id = 9) is homozygous for a rare allele.
y = halfCousinPed(degree = 1)
snp = marker(y, `9` = "a", alleles = c("a", "b"), afreq = c(0.01, 0.99))
plot(y, snp)
oneMarkerDistribution(y, ids = 8, partialmarker = snp)
|
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