View source: R/mutationMatrix.R
mutationMatrix | R Documentation |
Construct mutation matrices for pedigree likelihood computations.
mutationMatrix(
model = c("custom", "dawid", "equal", "proportional", "random", "onestep", "stepwise",
"trivial"),
matrix = NULL,
alleles = NULL,
afreq = NULL,
rate = NULL,
seed = NULL,
rate2 = NULL,
range = NULL,
transform = NULL,
validate = TRUE
)
validateMutationMatrix(mutmat, alleles = NULL)
model |
A string: either "custom", "dawid", "equal", "proportional", "random", "onestep", "stepwise" or "trivial". |
matrix |
When |
alleles |
A character vector (or coercible to character) with allele
labels. Required in all models, except "custom" if |
afreq |
A numeric vector of allele frequencies. Required in model "proportional". |
rate |
A number between 0 and 1. Required in models "equal", "proportional", "stepwise" and "onestep". |
seed |
A single number. Optional parameter in the "random" model, passed
on to |
rate2 |
A number between 0 and 1. The mutation rate between integer alleles and microvariants. Required in the "stepwise" model. |
range |
A positive number. The relative probability of mutating n+1 steps versus mutating n steps. Required in the "stepwise" and "dawid" models. Must be in the interval (0,1) for the "dawid" model. |
transform |
Either NULL (default) or one of the strings "MH", "BA", "PR", "PM". See Details. |
validate |
A logical (default: TRUE) indicating whether to validate custom models. |
mutmat |
An object of class |
Descriptions of the models:
custom
: Allows any mutation matrix to be provided by the user, in the
matrix
parameter.
dawid
: A reversible model for integer-valued markers, proposed by Dawid
et al. (2002).
equal
: All mutations equally likely; probability 1-rate
of no
mutation.
proportional
: Mutation probabilities are proportional to the target
allele frequencies.
random
: This produces a matrix of random numbers, where each row is
normalised so that it sums to 1. If rate
(and afreq
) is provided, the
mutation matrix is conditional on the overall mutation rate.
onestep
: A mutation model for markers with integer alleles, allowing
mutations only to the nearest neighbours in the allelic ladder. For example,
10
may mutate to either 9
or 11
, unless 10
is the lowest allele, in
which case 11
is the only option. This model is not applicable to loci with
non-integer microvariants.
stepwise
: A common model in forensic genetics, allowing different
mutation rates between integer alleles (like 9
) and non-integer
microvariants (like 9.3
). Mutation rates also depend on step size, as
controlled by the range
parameter.
trivial
: The identity matrix, implying that no mutations are possible.
If transform
is non-NULL, the indicated transformation is applied to the
matrix before returning. Currently, there are 4 available options:
MH
, BA
, PR
: See makeReversible()
PM
: See makeStationary()
An object of class mutationMatrix
, essentially a square numeric
matrix with various attributes. The matrix has entries in [0, 1]
and all
rows sum to 1. Both row names and column names are the allele labels.
mutationMatrix("equal", alleles = 1:3, rate = 0.05)
mutationMatrix("random", afreq = c(a=0.3, b=0.7), rate = 0.05, seed = 1)
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