NEW FEATURES
o [09-06-2026] Added methylation-scale support for beta, M-value, and copy
number phenotype inputs while retaining beta values for cell-composition
estimation and clock-foundation inputs.
o [09-06-2026] Improved methylationGLM and methylationLME throughput with
backend-aware CpG batching, Linux fork support, PSOCK fallback, and
fit-time summary caching while preserving the glm2 and lmerTest/lme4 model
engines.
o [09-06-2026] Added optional nlme-backed methylationLME fitting through
LME_LIBS/lmeLibs, with none, AR1, and CAR1 residual correlation choices
while preserving existing LME inputs, output files, and result classes.
o [09-06-2026] Added LME_CORRELATION_VAR/correlationVar so nlme AR1 and
CAR1 residual structures can use an explicit within-person ordering
variable.
o [09-06-2026] Updated methylationLME fixed-effect assembly so longitudinal
models are built from phenotypes, covariates, phenotype-specific PRS
terms, and optional interactions.
o [07-06-2026] Made the svaEnmix matrix plot adapt to larger
surrogate-variable matrices, paginate oversized matrices, and suppress
oversized SentrixID legends with an explicit log note.
o [07-06-2026] Renamed cross-reactive probe inputs to probe-exclusion inputs,
with support for multiple files and optional EPICv2 manifest flags.
o [06-06-2026] Added IDAT_FORCE to optionally force minfi IDAT parsing for
validated mixed-size IDAT inputs.
o [05-06-2026] Added configurable cross-reactive probe ID detection.
o [30-05-2026] Added a overview vignette with visual summaries of the main
dnaEPICO functions.
o [23-05-2026] Added a Quarto dashboard report workflow for dnamReport().
o [14-04-2026] Introduced a modular and reproducible pipeline for preprocessing
Illumina DNA methylation array data (EPICv2, EPIC and 450K).
o [18-02-2026] Initial Bioconductor submission of the dnaEPICO package.