FORCE {forrel} | R Documentation |
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 ofA1
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)
Source
Tillmar et al. The FORCE Panel: An All-in-One SNP Marker Set for Confirming Investigative Genetic Genealogy Leads and for General Forensic Applications. Genes. (2021)
Examples
x = setSNPs(nuclearPed(), snpData = FORCE)
summary(x)
getMap(x, markers = 1:3)
getFreqDatabase(x, markers = 1:3)