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