NEWS

---

AllelicSeries 1.1.5

• Updated COAST to automatically add an intercept to the covar matrix if one is not detected. Likewise for CalcSumstats.

AllelicSeries 1.1.1

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

AllelicSeries 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.

AllelicSeries 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.

AllelicSeries 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.

AllelicSeries 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.

AllelicSeries 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.