FamiliasLocus: Creates an object with information on a locus, including its...

In Familias: Probabilities for Pedigrees Given DNA Data

Creates an object with information on a locus, including its mutation matrices

Description

The user provides input needed to define an autosomal locus (also called system or forensic marker) to be used for pedigree calculations. The input is checked and if no errors are found a list with class FamiliasLocus is returned containing the information.

Usage

FamiliasLocus(frequencies, 
              allelenames, 
              name, 
              MutationModel = "Stepwise", 
              MutationRate  = 0, 
              MutationRange = 0.5, 
              MutationRate2 = 0, 
              MutationMatrix, 
              Stabilization = "None", 
              MaxStabilizedMutrate = 1, 
              femaleMutationModel, 
              femaleMutationRate, 
              femaleMutationRange, 
              femaleMutationRate2, 
              femaleMutationMatrix, 
              maleMutationModel, 
              maleMutationRate, 
              maleMutationRange, 
              maleMutationRate2, 
              maleMutationMatrix)

Arguments

frequencies	The first input of FamiliasLocus may be either a vector containing allele frequencies, or a previously created FamiliasLocus object. In the first case, the vector may include a possible silent allele; that it is silent is indicated in the allelenames. The frequencies must sum to 1. In the second case, the new object will be identical to the old object in terms of frequencies, names of alleles, and name of locus, so the 'allelenames' and 'name' parameters must be missing. However, at least one Mutation parameter or the Stabilization parameter must be non-missing, and new mutation matrices will be constructed based on these. If all Mutation parameters are missing, stabilized mutation matrices will be produced based on the mutation matrices of the old object.
allelenames	Names of the alleles, like 15 or 'A'. Note that the last allele may be called 'Silent' (or 'silent'). It is then treated as a silent allele in subsequent likelihood calculations. The default is to use the names attribute of the frequencies, if it exists; otherwise the default is to use consecutive integers, starting at 1. Note that if the 'Stepwise' mutation model is used, allele names (except for a silent allele) must be integers, with microvariants named as for example 15.2.
name	Characters like 'D3S1358', used to identify the locus (marker). The default is to use the name of the frequencies argument to this function.
MutationModel	The mutation model, used to create the mutation matrix. It may be 'Equal', 'Proportional', 'Stepwise', or 'Custom', see Details.
MutationRate	The mutation rate; for the 'Stepwise' model the rate of integer-step mutations. It is not used when the MutationModel is 'Custom'.
MutationRange	Only used when the MutationModel is 'Stepwise'. It then indicates the relative probability of mutating n+1 steps versus mutating n steps.
MutationRate2	Only used when the MutationModel is 'Stepwise'. It then indicates the rate of non-integer-step mutations, e.g., mutations from an allele with an integer name to alleles with decimal names indicating microvariants.
MutationMatrix	Only used when the MutationModel is 'Custom'. It then directly specifies the mutation matrix.
Stabilization	The possible values are 'None', 'DP', 'RM', and 'PM', with 'None' being the default. The other values adjust the mutation matrices so that allele frequencies after one or more generations of mutations will be equal to the original allele frequencies. See Details.
MaxStabilizedMutrate	Not used when stabilization is 'None'. Otherwise it indicates an upper bound for the specific mutation rate for each allele allowed in the mutation matrices after stabilization.
femaleMutationModel	Specifies a separate female value for MutationModel; defaults to MutationModel.
femaleMutationRate	Specifies a separate female value for MutationRate; defaults to MutationRate.
femaleMutationRange	Specifies a separate female value for MutationRange; defaults to MutationRange.
femaleMutationRate2	Specifies a separate female value for MutationRate2; defaults to MutationRate2.
femaleMutationMatrix	Specifies a separate female value for MutationMatrix; defaults to MutationMatrix.
maleMutationModel	Specifies a separate male value for MutationModel; defaults to MutationModel.
maleMutationRate	Specifies a separate male value for MutationRate; defaults to MutationRate.
maleMutationRange	Specifies a separate male value for MutationRange; defaults to MutationRange.
maleMutationRate2	Specifies a separate male value for MutationRate2; defaults to MutationRate2.
maleMutationMatrix	Specifies a separate male value for MutationMatrix; defaults to MutationMatrix.

Details

The probabilities for when and how mutations happen can be specified in mutation matrices, where the row corresponding to an allele indicates the probabilities that the allele is transferred as the allele indicated by the column. Mutation matrices may be specified directly in the MutationMatrix parameters by setting the value of the MutationModel parameter to 'Custom'. Otherwise they are computed based on the values of the MutationModel, MutationRate, MutationRate2, and MutationRange parameters. If MutationModel is 'Equal', there is an equal probability of mutating to any non-silent allele, given that a mutation happens. This model is referred to as 'Equal probability (simple and fast)' in Familias 2.0. If MutationModel is 'Proportional', the probability of mutating to any non-silent allele is proportional to its frequency. It is referred to as 'Probability proportional to frequency (stable)' in Familias 2.0. If MutationModel is 'Stepwise', it is required that the names of all non-silent alleles are positive integers, indicating the number of sequence repetitions of an STR marker, or decimal numbers with a single decimal, such as '15.2', indicating a microvariant. Mutations are then divided into two types: Those that add or subtract an integer to the allele, and those that add or subtract some fractional amount. The rate of these two types of mutations are given separately as MutationRate and MutationRate2, respectively. Relative probabilities of different mutatitons of the first type are specified using the MutationRange parameter. The model with only integer alleles is referred to as 'Probability decreasing with range (equal)' in Familias 2.0, while the more general model is called 'Extended stepwise' in Familias 3.0. Note that the probability of mutations to or from silent alleles is set to zero in all models except the 'Custom' model. For the mutation matrix of the 'Custom' model, the row names and column names of the matrix must coincide and be equally sorted. Furthermore, the allele names must be the same as the row names (and hence column names) of the mutation matrix and be equally sorted.

The 'Stabilization' parameter may be used to change the mutation matrices so that they become stationary relative to the frequencies vector. See the references. When the 'PM' setting is used together with the 'Stepwise' MutationModel and all allele names are integers, the resulting model is referred to as 'Probability decreasing with range (stable)' in Familias 2.0.

Value

A list of class FamiliasLocus containing

locusname	The name of the locus.
alleles	The frequencies of the alleles. The names of the alleles are included as the vector names.
femaleMutationType	A string specifying the type of the female mutations.
femaleMutationMatrix	The mutation matrix used for female transfer.
maleMutationType	A string specifying the type of the male mutations.
maleMutationMatrix	The mutation matrix used for male transfer.
simpleMutationMatrices	Indicates whether the probability of mutating to an allele is always independent of which allele the mutation happens from. If this is true, some likelihood computations can be done faster.
Stabilization	The stabilization method used.

References

Egeland, Kling, Mostad: Relationship Inference with Familias and R. (Academic press, 2016, https://www.familias.name/book.html). Simonsson, Mostad: Stationary Mutation models (FSI: Genetics, 2016).

Examples

#Simple examples
FamiliasLocus(1:4/10)
FamiliasLocus(frequencies = c(0.1, 0.2, 0.3, 0.4),
allelenames = c("A", "B", "C", "D"), name = "locus1")

#Modified to include a silent frequency
FamiliasLocus(frequencies = c(0.1, 0.2, 0.3, 0.3, 0.1),
allelenames = c("8", "9", "10", "11", "silent"), name = "locus1")

#Mutation rates added
FamiliasLocus(frequencies = c(0.1, 0.2, 0.3, 0.4),
allelenames = c("8", "9", "10", "11"), name = "locus1", 
femaleMutationRate = 0.001, maleMutationRate = 0.005)

#Mutation matrices specified directly 
MM <- matrix(c(0.99, 0.005, 0.003, 0.002, 0.005, 0.99, 0.005, 0, 
               0, 0.005, 0.99, 0.005, 0.002, 0.003, 0.005, 0.99), 
             ncol = 4, nrow = 4, byrow = TRUE)
FamiliasLocus(frequencies = c(0.1, 0.2, 0.3, 0.4), 
allelenames= c("08", "09", "10", "11"), name = "locus1", 
MutationModel = "Custom", MutationMatrix = MM)

#A locus is first created, and then edited
loc <- FamiliasLocus(c(0.2, 0.5, 0.3))
loc2 <- FamiliasLocus(loc, maleMutationRate = 0.001)
FamiliasLocus(loc2, Stabilization = "PM")

#A locus using standard Norwegian frequencies is created
data(NorwegianFrequencies)
FamiliasLocus(NorwegianFrequencies$TH01)

Familias documentation built on May 29, 2024, 10:49 a.m.