- Updated
COAST
andCOASTSS
to return estimated effect sizes and standard errors from the allelic series burden test.
- Added the ability to run
COAST
andCOASTSS
, 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.