forrel (version 1.8.1)

FORCE: FORCE panel SNP data

Description

Data frames describing the FORCE panel of SNPs for forensic genetics (Tillmar et al., 2021). We provide here two subsets of the complete panel: the autosomal kinship SNPs (FORCE, n = 3930) and the X-chromosomal SNPs (XFORCE, n = 246). To attach the markers to a pedigree, use pedtools::setSNPs() (see Examples).

Usage

FORCE
XFORCE

Format

Both FORCE and XFORCE are data frames with the following columns:

• CHROM: Chromosome

• MARKER: Marker name (rs number)

• MB: Physical position in megabases (GRCh38)

• A1: First allele

• A2: Second allele

• FREQ1: Allele frequency of A1

Details

Allele frequencies were retrieved from Ensembl using the REST API, with the population 1000GENOMES:phase_3:ALL as primary source. For 9 SNPs where this was unavailable, gnomADg:ALL was used instead.

One SNP - rs2323964 - was excluded due to lack of Ensembl/dbSNP support.

For details, the code used to download and process the data is available in the data-raw folder on GitHub: https://github.com/magnusdv/forrel/tree/master/data-raw

Note: The autosomal dataset (FORCE) was updated in version 1.8.1, adding 15 markers that were previously missing and revising some frequencies. The previous version is available via:

pth = system.file("extdata/FORCE_old.txt", package = "forrel")
oldforce = read.table(pth, header = TRUE)

Examples

x = setSNPs(nuclearPed(), snpData = FORCE)
summary(x)

getMap(x, markers = 1:3)
getFreqDatabase(x, markers = 1:3)