Description Usage Arguments Details Value Examples
View source: R/init_mutmodel.R
Method to initialise a mutation model.
1 2 3 | init_mutmodel(modeltype = 1, mutpars = NULL, ...)
## S3 method for class 'mutmodel'
print(x, ...)
|
modeltype |
1: SMM (traditional single-step mutation model). 2: LMM (Logistic mutation model introduced in Jochens (2011) 'Empirical Evaluation Reveals Best Fit of a Logistic Mutation Model for Human Y-Chromosomal Microsatellites'). 3: Exponential mutation model (unpublished). |
mutpars |
A matrix specifying the mutation parameters for each locus. Rows are parameters and columns are loci. If a vector, the same values are used for all loci. |
x |
A |
... |
not used. |
Mutation parameters for each locus.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 | Mutmodel 1 (SMM): 2 parameters per locus
P(i -> i-1) = mu\_d
P(i -> i+1) = mu\_u
P(i -> i) = 1 - P(i -> i-1) - P(i -> i+1)
= 1 - mu\_d - mu\_u
mutpars[1, locus]: mu\_d
mutpars[2, locus]: mu\_u
Mutmodel 2 (LMM): 6 parameters per locus
P(i -> i-1) = gamma\_d / (1 + exp(alpha\_d*(beta\_d - i)))
P(i -> i+1) = gamma\_u / (1 + exp(alpha\_u*(beta\_u - i)))
P(i -> i) = 1 - P(i -> i-1) - P(i -> i+1)
mutpars[1, locus]: gamma\_d
mutpars[2, locus]: alpha\_d
mutpars[3, locus]: beta\_d
mutpars[4, locus]: gamma\_u
mutpars[5, locus]: alpha\_u
mutpars[6, locus]: beta\_u
Mutmodel 3 (EMM): 4 parameters per locus
P(i -> i-1) = 1/((1 + exp(a + b*i))*(1 + exp(alpha + beta*i)))
P(i -> i+1) = exp(alpha+beta*i)/((1+exp(a+b*i))*(1+exp(alpha+beta*i)))
P(i -> i) = 1 - P(i -> i-1) - P(i -> i+1)
= exp(a + b*i)/(1 + exp(a + b*i))
mutpars[1, locus]: a
mutpars[2, locus]: b
mutpars[3, locus]: alpha
mutpars[4, locus]: beta
|
A mutmodel
object (a list with entires modeltype
and mutpars
).
1 2 3 4 5 6 7 8 9 10 11 12 | mutpars <- matrix(c(c(0.003, 0.001), rep(0.004, 2), rep(0.001, 2)), ncol = 3)
colnames(mutpars) <- c("DYS19", "DYS389I", "DYS391")
mutmodel <- init_mutmodel(modeltype = 1L, mutpars = mutpars)
mutmodel
mutpars.locus1 <- c(0.149, 2.08, 18.3, 0.149, 0.374, 27.4) # DYS19
mutpars.locus2 <- c(0.500, 1.18, 18.0, 0.500, 0.0183, 349) # DYS389I
mutpars.locus3 <- c(0.0163, 17.7, 11.1, 0.0163, 0.592, 14.1) # DYS391
mutpars <- matrix(c(mutpars.locus1, mutpars.locus2, mutpars.locus3), ncol = 3)
colnames(mutpars) <- c("DYS19", "DYS389I", "DYS391")
mutmodel <- init_mutmodel(modeltype = 2L, mutpars = mutpars)
mutmodel
|
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