NEWS.md
DsASC class inherits from DsAcc and holds reference and alternative counts at heterozygous SNPs alongside the ordinary peak accessibility matrix. buildMasterSNPs() builds a shared het-site list across donors and DsASC.gatk() counts alleles against it from WASP-corrected BAM files.calcASCStatistics() tests each site for allelic imbalance with a two-sided binomial test against 0.5 and per-sample BH correction.ascDropHomozygous(), ascFilterRegions(), ascPoolReplicates() and filterForRecurrence().ascAggregate(), ascSitePosterior(), ascSharing() and estimateSharedImbalance().plotASCBalance(), plotASCVolcano() and plotASCManhattan().prepareMotifmatchr() now supports JASPAR2020 (motifs = "jaspar2020").inst/extdata built by inst/scripts/make_vignette_data.R.R/AllGenerics.R instead of behind if (!isGeneric(...)) guards in each class file. The guards resolved the name through the search path, so a second devtools::load_all() in the same session skipped setGeneric() and the following setMethod() failed with “no existing definition”. devtools::check() is repeatable now.prepareMotifmatchr() read the species with provider(), which returns the BSgenome provider (“UCSC”) rather than the organism, and getMatrixSet() then failed. It uses BiocGenerics::organism() instead.filterForRecurrence() averaged log2FC_norm, a column calcASCStatistics() does not produce. It now uses log2FC_norm when present and log2FC otherwise.filterForRecurrence() no longer calls stringr::str_extract() when parsing a donor out of sampleId; stringr is not a declared dependency.NEWS.md and inst/CITATION, so citation("ChrAccR") returns a proper entry.DESCRIPTION gains URL and BugReports, which pkgdown uses for the site and for cross-package links.pkgdown/_pkgdown.yml; only the root _pkgdown.yml was ever read.overview and singlecell vignettes call getChromVarDev() with motifs = "jaspar2018". The old "jaspar" no longer matches a motif set now that the JASPAR versions are selected by name.