Allele Frequency Data for Human Genetic Markers

Provides allele frequency data for Short Tandem Repeat human genetic markers commonly used in forensic genetics for human identification and kinship analysis. Includes published population frequency data from the US National Institute of Standards and Technology, Federal Bureau of Investigation and the UK government.

Introduction

The forensicpopdata package provides allele frequency data for human genetic markers (STRs) commonly used in forensic genetics and kinship analysis. Currently three data sets are included:

• FBI 2015 FBI Population Data for the expanded CODIS core STR loci (FBI2015freqs)
• NIST 1036 Allele Frequency Data for 29 STR Loci (NIST1036freqs)
• UK DNA-17 Allele Frequency Data for 16 STR Loci (UKDNA17freqs)

In addition, it is possible to access the STRidER database through the read_STRidER_xml function.

Installation

The forensicpopdata package is not yet available from CRAN. You can install the forensicpopdata package using the pak package in R:

# install.packages("pak")
pak::pak("mkruijver/forensicpopdata")

Usage (data sets)

The data function is used to load a data set.

require(forensicpopdata)
#> Loading required package: forensicpopdata

data(NIST1036freqs)

The data set is a named list for each population:

names(NIST1036freqs)
#> [1] "AfAm"  "Asian" "Cauc"  "Hisp"

For each population, a list of frequencies by locus name is available:

NIST1036freqs$AfAm$TH01
#>           5           6           7           8           9         9.3 
#> 0.004385965 0.131578947 0.407894737 0.195906433 0.159356725 0.096491228 
#>          10 
#> 0.004385965

Usage (STRidER)

The read_STRidER_xml function downloads the most recent STRidER database from https://strider.online/.

freqs <- read_STRidER_xml()

The data set is a named list for each population:

names(freqs)
#>  [1] "Entire Database"        "Africa"                 "America"               
#>  [4] "Asia"                   "Europe"                 "AUSTRIA"               
#>  [7] "BELGIUM"                "BOSNIA AND HERZEGOWINA" "CZECH REPUBLIC"        
#> [10] "DENMARK"                "DOMINICAN REPUBLIC"     "FINLAND"               
#> [13] "FRANCE"                 "GERMANY"                "GREECE"                
#> [16] "HUNGARY"                "IRELAND"                "KENYA"                 
#> [19] "MONTENEGRO"             "NORWAY"                 "POLAND"                
#> [22] "SAUDI ARABIA"           "SLOVAKIA"               "SLOVENIA"              
#> [25] "SOUTH AFRICA"           "SPAIN"                  "SWEDEN"                
#> [28] "SWITZERLAND"            "THAILAND"               "VIETNAM"

For each population, a list of frequencies by locus name is available:

freqs$`Entire Database`$TH01
#>         8.3          10         7.3           7        10.3           8 
#> 3.58038e-04 2.72467e-02 3.58038e-05 2.26924e-01 3.58038e-05 1.13426e-01 
#>          12         9.3          11           6           4           9 
#> 1.43215e-04 2.01862e-01 6.44468e-04 1.93305e-01 3.58038e-05 2.35231e-01 
#>           5        13.3 
#> 7.16076e-04 3.58038e-05