locater is an R package for testing tree structures (represented via a set of discrete clades and/or a relatedness matrix) for association with traits of interest. Please see our pre-print describing the underlying LOCATER methodology here: https://www.biorxiv.org/content/10.1101/2024.09.30.615852 . We recently applied locater to a richly phenotyped whole genome sequencing described in our pre-print here https://www.medrxiv.org/content/10.1101/2024.11.04.24316696.
Please see the package website, https://ryanchrist.github.io/locater/ , for documentation and an Article presenting toy example for getting started: https://ryanchrist.github.io/locater/articles/simple_gwas_example.html . This article also demonstrates how the locater package API may be used to test inferred clades and relatedness matrices generated by other ancestry inference methods. The scripts used to generate the simulation results presented in our pre-print can be found here: https://github.com/ryanchrist/locater_paper_scripts .
While locater natively interacts with the local ancestry inference software package kalis, available here https://github.com/louisaslett/kalis/, the package exports functions exposing all internal testing routines so that LOCATER may be used in conjunction with other local genealogy inference engines/software. The exported function TestLoci is a wrapper function used for testing target variants along a chromosome; it provides a template for users hoping to adapt locater to use a different ancestry inference engine or otherwise customize the testing routine.
Try out locater via Docker
To try out locater immediately, check out our docker image available at https://hub.docker.com/repositories/rchrist7 . On a system with Docker installed, R can be launched in a interactive session under this image by running:{bash docker, eval=FALSE} docker run -it rchrist7/mini-shark /bin/bash R Call require(locater) in the R session to load locater. To get started, a simple vignette is available under the Articles tab at https://ryanchrist.github.io/locater/ alongside the documentation.
Installation Instructions
For those aiming to install locater on their own system or image, please follow the steps below.
Install R
If not already installed, please visit https://posit.co/download/rstudio-desktop/ for guidance. Once R is installed, we suggest installing them in the order below by copying and pasting the following R commands into R.
Install kalis
Our default ancestry inference engine kalis may be installed from our public Github repository as follows.
if(!require("BiocManager", quietly = TRUE)){install.packages("BiocManager")}
# install rdhf5, this requires zlib (if not already installed, try sudo apt install zlib1g-dev on Linux; brew install zlib on MacOS)
BiocManager::install("rhdf5") # a suggested dependency for kalis that will be required for running locater
install.packages("remotes")
remotes::install_github("louisaslett/kalis",
configure.vars = c(kalis = "PKG_CFLAGS='-march=native -mtune=native -O3'"))
if(!require(kalis)){stop("kalis was not properly installed")}Install Dependencies from public r-universe respository
```{r install_from_r_universe,eval=FALSE} install.packages(“RcppRoll”) install.packages(“QForm”, repos = “https://ryanchrist.r-universe.dev”, dependencies=TRUE) if(!require(QForm)){stop(“Qform was not properly installed”)}
install.packages(“renyi”, repos = “https://ryanchrist.r-universe.dev”) if(!require(renyi)){stop(“renyi was not properly installed”)}
## Install LOCATER from GitHub
```{r install_locater,eval=FALSE}
remotes::install_github("ryanchrist/locater")
if(!require(locater)){stop("locater was not properly installed")}Vignettes
Please see the introductory package vignette here https://ryanchrist.github.io/locater/articles/simple_gwas_example.html . This vignette provides a simple example deploying locater and a demonstration of how the locater package API can be used to test inferred clades and relatedness matrices generated by other ancestry inference methods. The source code is available in vignettes/simple_locater_example.Rmd . This vignette can also be built and viewed in R by calling the following.
{r build_vignette,eval=FALSE} remotes::install_github("ryanchrist/locater", build_vignettes=TRUE) vignette("simple_locater_example",package="locater")