Changelog • gwasRtools

gwasRtools 0.1.7 (9 July 2024)

get_loci() and get_nearest_gene() detect GWAS CATALOG input automatically. Can be disabled with detect_headers=FALSE

Change URL to reflect my GitHub username change from lukepilling to lcpilling to be more consistent between different logins, websites, and social media
https://lcpilling.github.io/gwasRtools
https://github.com/lcpilling/gwasRtools

get_loci() and get_nearest_gene() detect BOLT-LMM, SAIGE and REGENIE input automatically. Can be disabled with detect_headers=FALSE

get_loci() option get_ld_indep is renamed ld_clump to be more consistent with the {ieugwasr} package (https://github.com/MRCIEU/ieugwasr)
get_loci() option ld_pruning_r2 is renamed ld_clump_r2 to be more consistent with the {ieugwasr} package (https://github.com/MRCIEU/ieugwasr)
get_loci() option exclude_hla is renamed single_hla_locus because we are not actually excluding it, just treating it as one continuous locus

get_loci() now has the option exclude_hla to treat the HLA region as one continuous locus (default = FALSE). Coordinates are specified with hla_pos = c(25e6, 34e6) [these are the defaults]
Minor documentation updates

Added gwas_example data for running examples
get_loci() Genetic loci are now defined around variants with p-value < 5 × 10−8. The locus borders were set 500kb (n_bases) to each side of the highest genome-wide significant variant in each region.
get_loci() “lead” column is the best lead SNP from distance (i.e., all input SNPs) or from LD clumping (subset in reference dataset panel)
Fixes for get_loci() niche cases
Fixes for get_nearest_gene() niche cases

Fix internal -log10p calculation
Swap most “Depends” to “Imports”
Add dependency for {ieugwasr}
Add ld_clump option to get_loci() function, to get independent SNPs at the same locus
Add use_pvalue option to get_loci() function