NEWS.md
NEW FEATURES
o [09-08-2026] Added GENCODEHub annotation through AnnotationHub and
rebuilt the Quarto report dashboard with contextual figure and
workbook notes.
o [08-08-2026] Added SVA, GLM, LME, Manhattan, Venn/intersection, and
model-variable figures with selectable report browsers and ENmix controls
integrated into Quality Control.
o [08-08-2026] GLM and LME models now support optional coefficient and
omnibus phenotype Venn outputs with expanded factor terms, positional
labels, UCSC and GENCODE v50 figures, and ordered workbook sheets.
o [07-08-2026] Expanded GLM, lmerTest/lme4, and nlme visualisations and the
Quarto report with model-design and distribution diagnostics,
annotated-result Manhattan and optional model-level Venn plots,
selectable workbook sheets, and right-aligned navigation.
o [05-08-2026] GLM analyses now support optional omnibus F tests for
phenotype and phenotype-by-interaction terms.
o [05-08-2026] The Makefile configuration now uses model-specific
covariate, factor, and scaling variables for GLM and LME analyses.
o [05-08-2026] Added modelSections to dnamReport() for preprocessing-only,
GLM-only, LME-only, or complete reports. The complete report remains the
default.NEW FEATURES
o [23-07-2026] Reduced GLM, lmerTest/lme4, and nlme EWAS memory use with
bounded response-block parallelism, memory-aware workers, and resumable
compact phenotype summaries instead of genome-wide full-model RDS files.
o [23-07-2026] Recorded conditions in one Model.Message column and reported
unavailable results through workbook metadata.
o [22-07-2026] Added lmerTest omnibus F tests for complete
phenotype main effects or phenotype-by-interaction terms, with
Satterthwaite or Kenward-Roger denominator degrees of freedom and
CpG-adjusted results in annotated LME workbooks and reports.
o [19-07-2026] Added scaleVars predictor standardisation, consistent
GLM/lme4/nlme metadata, single-file SVA phenotype updates,
ordered annotated workbooks, and source-defined report card titles.
o [18-07-2026] Added optional sex-mismatch removal.
o [14-07-2026] Improved dnamReport() with lightweight paged and filterable
tables, faster tab loading, and phenotype-labelled GLM, LME, and nlme
formula notes, with biological participant detection in the Data summary.
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 an 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] Started development of the dnaEPICO package.