NEWS.md
In AllelicSeries: Allelic Series Test

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

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

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.

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

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.

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.

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.