Changelog • methylumi

methylumi 2.59.3

methylumIDAT() reads IDAT files from per-slide subdirectories, which is the layout Illumina’s own software produces (<idatPath>/<Slide>/<Slide>_<Array>_Grn.idat). Both the file-presence check and the code that actually opened the files assumed a flat directory, so a nested run reported every sample as missing. Flat layouts are unaffected. If the same basename appears under more than one subdirectory the read now errors and lists the candidates rather than picking one. getBarcodes() had the same blind spot and is fixed too. (#19)
diagnostics() works on objects with no color-channel annotation, such as the bundled GoldenGate mldat. Three if (annotation(x) == "...") tests errored outright on a zero-length annotation, and past those, the plotting loop split probes on a COLOR_CHANNEL column that such objects do not have, so every panel would have been drawn from zero probes. The long-reported call to the non-existent plot.density() was real, on the same path, and is also fixed. (#23)
methylumi.bgcorr() explains itself when asked for noob correction on an object that has no out-of-band intensities. Objects built from GEO series matrices or GenomeStudio output via methylumiR() carry only methylated/unmethylated/p-value data; OOB probes come only from reading raw IDATs. This used to fail deep inside method dispatch with “unable to find an inherited method for ‘intensities.OOB’”. (#24)

The gamma-family background corrections — method = "goob", "gamma" and "mode" — have been removed. They called gamma.mle(), gamma.mode() and gamma.integral() from rGammaGamma, a GitHub-only package that is not available from CRAN or Bioconductor and was never declared as a dependency, so these methods have errored for years. Requesting one now produces an error saying so. method = "noob" (the default) is unaffected. (#18)

qc.probe.plot(), plotNAs() and plotProbeNAs() no longer use ggplot2’s deprecated qplot(). Plot output is unchanged except in plotNAs(), where the segment layer now maps linewidth rather than the also-deprecated size; scale_linewidth uses a linear palette where scale_size used an area one, so line widths differ slightly. (#40)
A pkgdown site is published to https://seandavi.github.io/methylumi/ from a GitHub Actions workflow. (#43)

The package installs again. lattice removed parallel() from its exports (it was renamed parallelplot() years ago, then deprecated, then made defunct). Because the import resolved at lazy-load time, this broke R CMD INSTALL for the whole package rather than just parplot(), and took several downstream packages with it.
QCdata() is no longer silently lost when a MethyLumiSet is subset. eSet’s [ method drops the QC slot, and the previous guard tried to subset it after that had already happened — NULL[, j, drop = FALSE] returns NULL without erroring, so the guard was a no-op. QC data is now captured before dispatch and reattached. Feature indices no longer apply to QC probes, which live in their own feature space; only sample selection does. As a consequence combine() no longer reports “Dropped control probes” when combining subsets.
The example dataset mldat no longer shares its assayData between copies. It had been saved with storageMode = "environment" instead of "lockedEnvironment", so x <- mldat; methylated(x) <- ... silently mutated the original. The assay values themselves are unchanged.
plotNegOob() works again. It had two independent ggplot2 breakages: scale_y_continuous(breaks = NA) (now NULL) and opts() (removed from ggplot2 years ago, now labs()).

.mclapply() is now a thin wrapper around BiocParallel::bplapply() instead of parallel::mclapply() behind a require(). mclapply() forks, so it degraded to serial on Windows regardless. The signature is unchanged, and parallel results are verified identical to serial results. Configure it the standard Bioconductor way, with BiocParallel::register().
require() calls inside package code have been replaced with declared imports, or with requireNamespace() guards that produce an actionable error for genuinely optional packages (MASS, Biostrings, lumi). require() returns FALSE rather than erroring, so a missing package used to change behaviour silently.
Bare T/F are now TRUE/FALSE throughout (105 occurrences). These are ordinary variables, not reserved words, so a user with a variable named T in scope could change the meaning of a default argument.
1:length(x), 1:nrow(x) and 1:ncol(x) are now seq_along()/seq_len(), which behave correctly when the length is zero.
Base-package functions used by the package are now properly imported, rather than resolving by accident because the packages happened to be attached.

Most man pages are generated from roxygen blocks now. The S4 class and generic documentation remains hand-written on purpose; see the note in R/data.R.
extractBarcodeAndPosition() was documented as returning three columns with numeric row and column. It returns five, and row/column are strings such as "R006"; the numeric ones are rowNumber/columnNumber.

The package has a test suite for the first time: 36 tests covering import from IDAT and text, normalization, background correction, coercions, filtering, subsetting and every plotting entry point.
CI runs R CMD check against Bioconductor devel on GitHub Actions, replacing a .travis.yml that had not run in years.

methylumi.bgcorr() with method = "gamma" or method = "mode" does not work. It calls gamma.mle(), gamma.mode() and gamma.integral() from rGammaGamma, which is not declared as a dependency and is not available from CRAN or Bioconductor. The default noob method is unaffected.
qc.probe.plot(), plotNAs() and plotProbeNAs() still use ggplot2’s deprecated qplot().