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.
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")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
#> 0.004385965The 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