NEWS

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crossarrayEWAS 0.99.1

• ewas_regions() and ewas_blocks() are new and are now the interface most analyses need: each takes a SummarizedExperiment or GenomicRatioSet and returns a GRanges, running the whole analysis the corresponding pipeline stage runs, including the within-subject permutation null and subject-level selection stability that previously existed only in the stage drivers.
• SummarizedExperiment, GenomicRanges, S4Vectors and IRanges moved from Suggests to Imports. The object interface is no longer optional.
• Assay selection: NULL now means the assay named M, or the only assay. This is what a GenomicRatioSet needs, since minfi stores Beta first. A beta-valued assay is converted to M-values with a message rather than analysed with a warning.
• Six numerical helpers (pinv(), demean_by_group(), demean_rows_by_group(), within_df(), fold_assign(), state_labels()) are internal: they were pipeline plumbing rather than part of the interface. The pipeline's stage drivers now source their own copy of the core instead of loading the package.
• NAMESPACE is generated by roxygen2 from @export and @importFrom tags, and roxygen Markdown is enabled, so help pages render links and code spans instead of raw Markdown.
• The vignette starts from an object rather than a matrix, adds an installation section, shows how to build the input from 450K and EPIC minfi objects with combineArrays(), analyses a real 2,000-probe subset of GSE237561 that now ships in inst/extdata, and compares the package with bumphunter, DMRcate, ENmix, coMethDMR, minfi::blockFinder(), limma::duplicateCorrelation() and variancePartition::dream().
• moderate_variance() no longer checks for limma with requireNamespace(); it is an Imports dependency.
• URL and BugReports point at the package repository, where users report issues, rather than at the pipeline that generates the package.

crossarrayEWAS 0.99.0

• First version, extracted from the ewas-crossarray-harmonise pipeline (bin/ewasml.R). Function bodies are unchanged from the pipeline source; the package adds documentation, a namespace and unit tests.