A function to calculate the genotype frequencies and the transition matrices
for the joint genotypes of two unlinked genetic loci in linkage
equilibrium, given the corresponding objects for the separate loci.
The results from this function can be used as inputs to
pedigree_loglikelihood or
genotype_probabilities
to model the combined effect of the two loci on phenotypes.
combine_loci(geno_freq1, geno_freq2, trans1, trans2, annotate = FALSE)A list with the following components:
A vector of strictly positive numbers (the joint genotype
frequencies) that sum to 1, with genotype names added when annotate is TRUE
Either a matrix of genetic transmission probabilities suitable to be
used as the trans argument of pedigree_loglikelihood
(if annotate is FALSE), or a data frame that is an annotated version of
this matrix (if annotate is TRUE).
A data frame giving the locus 1 and locus 2 genotypes
that correspond to each joint genotype. In some cases, this could aid the user's
calculation of the penet argument of pedigree_loglikelihood.
A vector of strictly positive numbers that sum to 1,
with geno_freq1[i] interpreted as the population genotype frequency of the
ith possible genotype at a genetic locus (locus 1).
When annotate is TRUE, the names of the genotypes at locus 1 will be
taken to be names(geno_freq1) or, if names(geno_freq1) is NULL, to be
1:length(geno_freq1).
Similar to geno_freq1 (above) but interpreted as the
population genotype frequencies for a different genetic locus (locus 2).
An ngeno1^2 by ngeno1 matrix of non-negative numbers
whose rows sum to 1, where ngeno1 = length(geno_freq1).
This matrix is usually generated by trans_monogenic or a similar
helper function, and its elements are interpreted as genetic
transmission probabilities for locus 1 (see trans_monogenic
for more details). If trans1 has ngeno1 + 2 instead of ngeno1 columns,
as could occur if it was generated by
trans_monogenic with annotate = TRUE, then the first two
columns will be deleted and trans1 will be converted to a matrix.
Similar to trans1 (above) but interpreted as the
genetic transmission probabilities for locus 2.
A logical flag. When FALSE (the default), the function
returns objects that can be used as the geno_freq and trans arguments of
pedigree_loglikelihood. When TRUE, the function annotates
these objects (and converts trans to a data frame) to make the output more
easily understood by humans.
This function combines the genotype frequencies and transition
probabilities of two unlinked genetic loci that are in linkage equilibrium
in a given population. Because
the loci are unlinked, any person's genotypes at the two loci are
conditionally independent given his or her parental genotypes,
and because the loci are in linkage equilibrium, the genotypes at the two
loci for a random person from the population are independent.
This function uses these assumptions to calculate the population frequencies
and transition probabilities for the joint genotypes of the two loci, where a
joint genotype is just a pair consisting of a genotype at locus 1
and a genotype at locus 2. If the annotate option is set to FALSE then
these frequencies and probabilities can be used in
pedigree_loglikelihood to model the combined effect of the two
loci on the phenotypes. By a repeated application of this function, more
than two genetic loci can be included in the genetic model.
pa1 <- c(0.9, 0.1); names(pa1) <- c("-","+")
pa2 <- c(0.5, 0.5); names(pa2) <- c("A","a")
(geno_freq1 <- geno_freq_monogenic(pa1, TRUE))
(geno_freq2 <- geno_freq_monogenic(pa2, TRUE))
(trans1 <- trans_monogenic(2, TRUE))
(trans2 <- trans_monogenic(2))
(cl <- combine_loci(geno_freq1, geno_freq2, trans1, trans2, TRUE))
sum(cl$geno_freq)
apply(cl$trans[,-(1:2)], 1, sum)
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