paramlink: Familias2linkdat – R documentation

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Familias2linkdat

Convert 'Familias' output to linkdat objects

Description

Familias is a widely used program for computations in forensic genetics. The function documented here facilitates the use of paramlink for specialized computations which are not implemented in Familias, e.g. conditional simulations.

Usage

Familias2linkdat(familiasped, datamatrix, loci)

readFamiliasLoci(loci)

connectedComponents(ID, FID, MID)

Arguments

`familiasped`	A `FamiliasPedigree` object or a list of such.
`datamatrix`	A data frame with two columns per marker (one for each allele) and one row per individual.
`loci`	A `FamiliasLocus` object or a list of such.
`ID`	An integer vector: Individual ID.
`FID`	An integer vector: ID of father.
`MID`	An integer vector: ID of mother.

Details

The Familias program represents pedigrees and marker data in a way that differs from paramlink in several ways, mostly because of paramlink's stricter definition of a 'pedigree'. In paramlink, a pedigree must be connected, have numerical IDs, and each member must have either 0 or 2 parents present in the pedigree. None of this is required by FamiliasPedigree objects. The conversion function Familias2linkdat takes care of all of these potential differences: It converts each FamiliasPedigree into a list of connected linkdat objects, additional parents are added where needed, and non-numerical ID labels are stored in the plot.labels slot of the linkdat object(s).

Value

A linkdat object, or a list of such.

Author(s)

Magnus Dehli Vigeland, Thore Egeland

References

Windows Familias is freely availabe from http://familias.name.

Examples

# Example
## Not run: 
library(Familias)
data(NorwegianFrequencies)
locus1 = FamiliasLocus(NorwegianFrequencies$TH01)
persons = c('mother', 'daughter', 'AF')
ped1 = FamiliasPedigree(id=persons, dadid=c(NA, 'AF', NA), momid=c(NA, 'mother', NA), 
                         sex=c('female', 'female', 'male'))
datamatrix = data.frame(THO1.1=c(NA, 8, NA), THO1.2=c(NA,9.3, NA))
rownames(datamatrix) = persons
x = Familias2linkdat(ped1, datamatrix, locus1)
plotPedList(list(x), new=TRUE, frametitles=c('H1'), available='shaded', marker = 1)

# Example
library(fam2r)
data(F21)
pedigrees = F21$pedigrees
datamatrix = F21$datamatrix
loci = F21$loci
x = Familias2linkdat(pedigrees, datamatrix, loci)
plotPedList(x, new=TRUE, frametitles=c('H1', 'H2'), available='shaded')

# Give dev.width explicitly to allow for long names
plotPedList(x, new=TRUE, frametitles=c('H1', 'H2'), available='shaded',
            dev.width=17)

# Numerical labels work better
plotPedList(x, new=TRUE, id.labels='num', frametitles=c('H1', 'H2'),
            available='shaded')

## End(Not run)

paramlink

Parametric Linkage and Other Pedigree Analysis in R

v1.1-2

GPL (>= 2)

Authors

Magnus Dehli Vigeland [aut, cre], Thore Egeland [ctb], Guro Doerum [ctb]

Initial release

2018-01-05