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NEWS.md

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Version 1.1.1

  • Updated COAST and COASTSS to return estimated effect sizes and standard errors from the allelic series burden test.

Version 1.1.0

  • Added the ability to run COAST and COASTSS, as well as the component tests, with an arbitrary number of discrete annotation categories.
    • The updated code prefers integer annotation category labels starting at 1. However, the main functions will still support 0-indexed category labels.
  • Updated the data generating process DGP to simulate data with an arbitrary number of annotation categories.
  • Added vignettes on Data Generation and COAST-SS.
  • Updated CalcSumstats to bind all variant-level information (annotations, MAFs, betas, standard errors, p-values) into a single dataframe.

Version 1.0.2

  • Streamlined and simplified the summary statistic-based allelic series baseline and sum tests, removing the need for meta-analysis or estimating cross category correlations.

Version 1.0.0

  • Added ability to run COAST starting from summary statistics:
    • ASBTSS runs the allelic series burden test from summary statistics.
    • ASKATSS runs the allelic series SKAT test from summary statistics.
    • COASTSS runs the omnibus coding-variant allelic series test from summary statistics.
  • Added a CalcSumstats function to generate summary statistics from individual-level data.

Version 0.6.0

  • Replaced the CountAlleles function with a similar (but faster) Counts function that returns counts the total number of alleles, variants, and carriers by variant class.
  • Updated the formatting of the results output by the main COAST function.

Version 0.5.0

  • Added option (min_mac) to filter the variant set to only include those variants having at least a minimum minor allele count (10 is recommended).
  • Added a function (CountAlleles) to count the number of alleles of each variant category present in the genotype matrix. Also allows for counting the number of carriers of each type of allele.
  • By default, COAST now reports the number of alleles of each variant category that contributed to the test.