NEWS

GPlinksR 0.99.2

Added optional mart, gene_map, and enhancer-coordinate arguments so users can select an Ensembl mirror or provide local mapping resources.
Added small, package-installed PEREGRINE example files for deterministic offline execution of build_gp_links().

Updated the minimum R version requirement to R 4.6.0.
Replaced the hard-coded chromosome list with GenomeInfoDb::standardChromosomes() for human sequence validation.
Added an explicit GenomicRanges import, declared IRanges as a runtime dependency, and refactored repeated input, cache, rowData, and peak-validation code into shared internal helpers.
Split long enhancer-building routines into focused internal helpers and normalized R source indentation to four-space multiples.
Avoided external chromosome-style lookups when aligning human sequence levels from EnsDb.Hsapiens.v86 with UCSC-style peak coordinates.

Added a package-level help page.
Added BiocManager installation instructions and executable, offline build_gp_links() examples to the vignette and function help page.
Documented the KPMP-derived example inputs and the source of the bundled PEREGRINE example records.

Added regression tests for standard chromosomes, local BioMart mapping, local enhancer coordinates, shared helpers, sequence-level handling, and packaged example consistency.

Added build_gp_links_wrapper() to support MultiAssayExperiment, SingleCellExperiment, and SummarizedExperiment inputs.
Added packaged example data via gp_example_inputs.
Added a Bioconductor-style vignette demonstrating direct and container-based workflows.

Improved build_gp_links() handling of empty overlap cases so sparse inputs return empty results instead of errors.
Updated the closest-gene mapping to use gene TSS positions.