README.md

In jk2236/RecordMatching: Statistical detection of relatives typed with disjoint forensic and biomedical loci

Record Matching

Description

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.

Platform

This is an R package that can work in any platform that makes use of R.

System Requirements

• BEAGLE 4.1
• Java version 8 - required by BEAGLE. See BEAGLE manual for details.
• VCFtools. conda version is also available here.

Dataset

• 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.

Installation

if (!require("devtools")) {
    install.packages("devtools")
}
devtools::install_github("jk2236/RecordMatching")
library(RecordMatching)

Example

• See the example documentation.
• The corresponding R markdown file can be found at here.

Reference

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

jk2236/RecordMatching documentation built on Dec. 21, 2021, 12:10 a.m.