famMix: Likelihood for mixtures with related contributors based on...

Description Usage Arguments Details Value Author(s) References See Also Examples

View source: R/famMix.R

Description

Likelihood for mixtures with related contributors based on Familias. For a general description of the problem, see paraMix. As opposed to paraMix this function uses the R version of Familias for likelihood calculation and therefore theta-correction, mutation models and silent allele frequencies (but not X-chromosomes or simulation) are accomodated.

Usage

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famMix(x, R, id.U, id.V = NULL, partialmarker = NULL, theta = 0, 
mutationRateFemale = 0, mutationRateMale = 0, 
mutationModelFemale = "stable", mutationModelMale = "stable", 
mutationRangeFemale = 0.1, mutationRangeMale = 0.1, 
silentFrequency = 0,check=TRUE)

Arguments

x

linkdat object.

R

Integers, mixture.

id.U

List of unknown contributors (e.g.,suspect(s)).

id.V

Integers indicating typed non-contributors.

partialmarker

A marker object.

theta

Real in [0,1]

mutationRateFemale

See FamiliasLocus.

mutationRateMale

See FamiliasLocus.

mutationModelFemale

See FamiliasLocus.

mutationModelMale

See FamiliasLocus.

mutationRangeFemale

See FamiliasLocus.

mutationRangeMale

See FamiliasLocus.

silentFrequency

Real in [0,1].

check

If TRUE check of input is performed and calculations stop if they are likely to take too much time.

Details

See paraMix.

Value

x

linkdat object updated with genotypes of missing individuals specified by id.U

likelihod

The likelood Pr(R,T,V|H)

allLikelihoods

Terms adding to above Pr(R,T,V|H)

Author(s)

Thore Egeland <[email protected]>

References

Egeland et al (2013)

See Also

paraMix

Examples

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#Example
require(paramlink)
require(Familias)

euroMix documentation built on May 29, 2017, 7:21 p.m.