mutationMatrix {pedmut} | R Documentation |
Mutation matrix
Description
Construct mutation matrices for pedigree likelihood computations.
Usage
mutationMatrix(
model = c("custom", "equal", "proportional", "random", "onestep", "stepwise",
"trivial"),
matrix = NULL,
alleles = NULL,
afreq = NULL,
rate = NULL,
seed = NULL,
rate2 = NULL,
range = NULL
)
validateMutationMatrix(mutmat, alleles = NULL)
Arguments
model |
A string: either "custom", "equal", "proportional", "random", "stepwise" or "onestep". |
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" model. |
mutmat |
An object of class |
Details
Descriptions of the models:
-
custom
: Allows any mutation matrix to be provided by the user, in thematrix
parameter. -
equal
: All mutations equally likely; probability1-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. -
onestep
: A mutation model for microsatellite markers, 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-integral microvariants. -
stepwise
: A common model in forensic genetics, allowing different mutation rates between integer alleles (like '16') and non-integer "microvariants" like '9.3'). Mutations also depend on the size of the mutation if the parameter 'range' differs from 1. -
trivial
: The identity matrix; i.e. no mutations are possible.
Value
A square matrix with entries in [0, 1]
, with the allele labels as
both colnames and rownames.
Examples
mutationMatrix(alleles = 1:3, model = "equal", rate = 0.05)