ensemblQueryR: fast, flexible and high-throughput querying of Ensembl LD API endpoints in R

TL;DR

ensemblQueryR is an R package that enables fast, flexible, and high-throughput querying of Ensembl LD API endpoints, optimizing performance and resource usage for genomic research workflows.

Contribution

It introduces a user-friendly R interface with optimized functions and parallelization for efficient large-scale LD data retrieval from Ensembl.

Findings

10-fold speed increase over existing tools

Uses one-third of the RAM compared to similar software

Compatible across operating systems via Docker and Singularity

Abstract

We present ensemblQueryR, a package providing an R interface to the Ensembl REST API that facilitates flexible, fast, user-friendly and R workflow integrable querying of Ensembl REST API linkage disequilibrium (LD) endpoints, optimised for high-throughput querying. ensemblQueryR achieves this through functions that are intuitive and amenable to custom code integration, use of familiar R object types as inputs and outputs, code optimisation and optional parallelisation functionality. For each LD endpoint, ensemblQueryR provides two functions, permitting both single-query and multi-query modes of operation. The multi-query functions are optimised for large query sizes and provide optional parallelisation to leverage available computational resources and minimise processing time. We demonstrate that ensemblQueryR has improved performance in terms of random access memory (RAM) usage and speed, delivering a 10-fold speed increase over analogous software whilst using a third of the RAM. Finally, ensemblQueryR is near-agnostic to operating system and computational architecture through availability of Docker and singularity images, making this tool widely accessible to the scientific community.