This R package contains tools for performing record matching of pairs of genetic profiles, as described in Kim et al. and Edge et al.. The pipeline starts with a set of reference files containing SNP-STR genotypes on reference individuals, a set of files containing STR profiles only on test individuals, a set of files containing SNP profiles only on test individuals, and a set of genetic map files. It outputs a match-score matrix for all STR-SNP pairs, with rows indicating STR profiles and columns indicating SNP profiles. The package also includes a function that processes the match-score matrix. It enables hypothesis tests for a variety of relatedness hypotheses based on SNP and STR profiles. For a demonstration of the pipeline using the package, please see Example.
This is an R package that can work in any platform that makes use of R.
- BEAGLE 4.1
- Java version 8 - required by BEAGLE. See BEAGLE manual for details.
- VCFtools.
condaversion is also available here.
- HGDP SNP-STR data containing 872 individuals can be downloaded from here.
- Human genetic maps. HapMap GrCh36 and GrCh37 genetic maps in PLINK format. Can be downloaded from BEAGLE page.
- All genotypes in the reference panel must be non-missing and phased for BEAGLE imputation.
Example dataset and genetic map files are included in the package for running Example.
if (!require("devtools")) {
install.packages("devtools")
}
devtools::install_github("jk2236/RecordMatching")
library(RecordMatching)- See the example documentation.
- The corresponding R markdown file can be found at here.
Kim J, Edge MD, Algee-Hewitt BFB, Li JZ, Rosenberg NA (2018). Statistical detection of relatives typed with disjoint forensic and biomedical loci. Cell, 175(3):848-858.e6. https://doi.org/10.1016/j.cell.2018.09.008
Edge MD, Algee-Hewitt BFB, Pemberton TJ, Li JA, Rosenberg NA (2017). Linkage disequilibrium matches forensic genetic records to disjoint genomic marker sets. PNAS, 114(22):5671-5676. https://doi.org/10.1073/pnas.1619944114