get_allele_freqs: Get Allele Frequencies in pedtools Format

In mispitools: Missing Person Identification Tools

Get Allele Frequencies in pedtools Format

Description

Converts allele frequency data from a data frame to a list format compatible with the pedtools package for pedigree analysis.

Usage

get_allele_freqs(region)

Arguments

region

A data frame containing allele frequencies. The first column should be "Allele" with allele designations, and subsequent columns should be marker names with frequency values. Available built-in databases: Argentina, Asia, Austria, BosniaHerz, China, Europe, Japan, USA.

Details

The function transforms the data frame format (rows = alleles, columns = markers) into the list format required by pedtools (one element per marker, named by allele). This enables seamless integration with pedigree likelihood calculations.

Value

A named list where each element represents a genetic marker. Each marker element is a named numeric vector with allele names and their corresponding frequencies. This format is directly compatible with pedtools::setMarkers().

Source

\Sexpr[results=rd]{tools:::Rd_expr_doi("10.1016/j.fsigss.2009.08.178")} \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1016/j.fsigen.2016.06.008")} \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1016/j.fsigen.2018.07.013")}

References

Marino M, et al. (2009). "Allele frequencies of 15 STRs in an Argentine population sample." Forensic Science International: Genetics Supplement Series. \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1016/j.fsigss.2009.08.178")}

See Also

Argentina, Europe, USA for available frequency databases, sim_lr_genetic for using these frequencies in simulations.

Examples

# Convert Argentina database to pedtools format
freqs <- get_allele_freqs(Argentina)

# Check available markers
names(freqs)

# Use with pedtools
library(pedtools)
library(forrel)
x <- linearPed(2)
x <- setMarkers(x, locusAttributes = freqs[1:5])

mispitools documentation built on Aug. 26, 2026, 1:08 a.m.