forrel: Familias2ped – R documentation

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Familias2ped

Convert Familias objects to ped format

Description

Familias is a widely used software for forensic kinship computations, which also features an accompanying R package (also called Familias). The function documented here converts pedigrees and marker data from the R version of Familias to pedtools::ped() format, used by forrel. This may be of interest for specialized computations not implemented in Familias, e.g. conditional simulations. Note: For importing ".fam" files created by (the stand-alone) Familias, see readFam().

Usage

Familias2ped(familiasped, datamatrix, loci, matchLoci = FALSE)

readFamiliasLoci(loci)

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.
`matchLoci`	A logical. If TRUE, the column names of `datamatrix` must be found either within `names(loci)` or within the `name` entries of `loci`. The column names of `datamatrix` are assumed to come in pairs with suffixes ".1" and ".2", e.g. "TH01.1", "TH01.2", etc. If FALSE (the default) it is assumed that the `loci` correspond to the (pairs of) columns in `datamatrix` sequentially.

Details

The Familias program represents pedigrees and marker data in a way that differs from the ped format in several ways, mostly because of the latter's stricter definition of a pedigree. A ped object always represent a connected pedigree, and each member must have either 0 or 2 parents. None of this is required by FamiliasPedigree objects. The conversion function Familias2ped takes care of all potential differences: It converts each Familias pedigree into a list of connected ped objects, adding missing parents where needed.

Value

A ped object, or a list of such.

Author(s)

Magnus Dehli Vigeland, Thore Egeland

References

Familias is freely available from https://familias.name.

Examples

famPed = structure(
  list(id = c('mother', 'daughter', 'AF'),
       findex = c(0, 3, 0),
       mindex = c(0, 1, 0),
       sex = c('female', 'female', 'male')),
  class = "FamiliasPedigree")

datamatrix = data.frame(
  M1.1 = c(NA, 8, NA),
  M1.2 = c(NA, 9.3, NA),
  row.names = famPed$id)

famLoc = structure(
  list(locusname = "M1",
       alleles = c("8" = 0.2, "9" = 0.5, "9.3" = 0.3)),
  class = "FamiliasLocus")

Familias2ped(famPed, datamatrix, loci = famLoc, matchLoci = TRUE)

forrel

Forensic Pedigree Analysis and Relatedness Inference

v1.3.0

GPL-3

Authors

Magnus Dehli Vigeland [aut, cre] (<https://orcid.org/0000-0002-9134-4962>), Egeland Thore [ctb]

Initial release