sLDtest

The sLDtest R package implements a hypothesis testing method of structural linkage disequilibrium (sLD), as well as a forward-generating probability model for genotypes in sLD.

Installation

install.packages("pak")
pak::pak("StoreyLab/sLDtest")

Examples

Input genotype data

sLDtest is designed to be applied to genotype data like in the example below. These genotypes were simulated under an admixture model with $K=4$ admixed populations using the package bnpsd.

library(sLDtest)

# Load input genotype data matrix (I loci by J individuals)
data(genodata)

Run the sLD test

The implementation of the sLD test requires only genotypes to be supplied by the user. However, individual-specific allele frequencies (IAFs) must be estimated from these genotypes using any one of a wide range of existing methods. In our analyses, we use the package alstructure to estimate IAFs.

X <- genodata
J_ind <- ncol(X) # get the number of individuals 

# Estimate IAFs 
library(devtools)
install_github("storeylab/alstructure")
library(alstructure)
Pi_hat <- alstructure::estimate_F(X, d = 4)$F_hat # assume K known for simplicity
Pi_hat[Pi_hat < 1/(2*J_ind)] <- 1/(2*J_ind) # truncate estimates
Pi_hat[Pi_hat > 1 - 1/(2*J_ind)] <- 1 - 1/(2*J_ind)

After estimating IAFs, we can compute sLD test statistics. The user supplies a list of locus pairs to perform the sLD test on as follows. Here, we simply randomly select 1000 pairs of loci.

n_pairs <- 1000
pair_ids <- t(replicate(n_pairs, sample(nrow(X), size = 2, replace = FALSE)))
test_stats <- sLD(X, Pi_hat, pair_ids)

We then compute $p$-values as follows. We use a Normal(0,1) null distribution by default, though we can also supply an empirical null distribution if necessary.

p_vals <- compute_p_val(test_stats)

To reproduce the results in the paper "A test for linkage disequilibrium in structured populations" by Alvin J. Zhang and John D. Storey, please visit the following repository:

https://github.com/StoreyLab/sLD-manuscript-analysis

Citations

Alvin J. Zhang, John D. Storey. 2026. "A test for linkage disequilibrium in structured populations." bioRxiv doi:10.64898/2026.10.18.759967 2026-10-19.

For users of alstructure, please cite: Irineo Cabreros, John D. Storey. 2019. "A likelihood-free estimator of population structure bridging admixture models and principal components analysis." doi: 10.1534/genetics.119.302159 2019-08-01.

For users of bnpsd, please cite: Alejandro Ochoa, John D Storey. 2021. "Estimating FST and kinship for arbitrary population structures." PLoS Genet 17(1): e1009241. PubMed ID 33465078. doi:10.1371/journal.pgen.1009241. bioRxiv doi:10.1101/083923 2016-10-27.