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NEWS.md

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gwasRtools 0.1.7 (9 July 2024)

Updates

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

Changes

  • Change URL to reflect my GitHub username change from lukepilling to lcpilling to be more consistent between different logins, websites, and social media

gwasRtools 0.1.6 (20 April 2024)

  • get_loci() -- update errors and use p-value if provided

gwasRtools 0.1.5 (6 March 2024)

  • Change how functions detect SAIGE input
  • Added warnings for depreciated options in get_loci()

gwasRtools 0.1.4 (17 Jan 2024)

Updates

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

Breaking changes

  • 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

gwasRtools 0.1.3 (27 Nov 2023)

  • 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

gwasRtools 0.1.2 (15 Sept 2023)

  • 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

gwasRtools 0.1.1 (30 Aug 2023)

  • 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

gwasRtools 0.1.0 (30 June 2023)

  • Added a NEWS.md file to track changes to the package.