NEWS

sesame 1.31.12

The Basic Usage vignette's note on the C implementation names it SeSAMe2 and links its current home (zhou-lab.github.io/sesame), gives the working conda line (sesame and yame from zhou-lab), and states the agreement with this package as measured on the shared annotation (QCDPB betas to about 1e-15 with sesameData >= 1.31.1).

The startup message no longer carries the knowYourCG pointer added in 1.31.10; the README and the Basic Usage vignette point to knowYourCG for enrichment of CpG sets instead.

The startup message points at the knowYourCG package for enrichment of CpG sets.

Documentation fixes from a review of the vignettes. The inference vignette shows its library(sesame) and caching setup, gives raw download URLs for the two clock files, states the mouse age the code returns (1.18 months) and re-identifies from ~/Downloads in both calls. The Basic Usage and QC vignettes define idat_dir as the built-in HM27 IDATs. The non-human vignette drops an undefined tmp and uses prep code SHCDPB, as the Basic Usage table recommends for Mammal40. Ethnicity is no longer listed as an inference in DESCRIPTION or the vignette.
sesameQCtoDF() works on HM27: the median beta statistics are unnamed, so an array without ch or rs probes no longer gives "row names contain missing values".
matchDesign() (prep code M) stops with an install line when the suggested package RPMM is missing.
inferSpecies() warns when fewer than 30% of the probes are detected, since the species call is then unreliable.

inst/CITATION writes the one non-ASCII author name (Szab\u00f3) as an escape, so utils::readCitationFile() reads the file without a declared encoding. BiocCheck warned "Unable to read CITATION file".

visualizeRegion() (and visualizeGene/visualizeProbes through it) can draw annotation tracks under the heatmap: show.cgi adds CpG context (island, shore, shelf, open sea, from UCSC cpgIslandExt) and show.regulatory adds Ensembl Regulatory Build features (needs biomaRt, in Suggests). Each track is built on first use and cached in BiocFileCache. show.beta.legend and show.annotation.legend add legends; show.loci with show.probeNames = FALSE labels probes by coordinate. All default to off, so existing calls draw as before. New sesameAnno_buildHeatmapAnnotations() builds the tracks. Contributed by Pancreas-Pratik (zwdzwd/sesame#220).

qualityMask()'s recommended set for HM450 and EPIC is now the five M_* tracks EPICv2 and MSA already use (M_1baseSwitchSNPcommon_5pt, M_2extBase_SNPcommon_5pt, M_mapping, M_nonuniq, M_SNPcommon_5pt), read from KYCG.HM450.Mask.20261008 / KYCG.EPIC.Mask.20261008 in sesameData, which are built from the InfiniumAnnotation v8.2 masks. The older KYCG tracks (mapping, channel_switch, snp5_GMAF1p, extension, sub30_copy) masked about twice as many probes and are still available through mask_names. This brings R and SeSAMe2 to the same quality mask on all four human arrays (zhou-lab/sesame#1). KYCG.EPICv2.Mask.20261008 and KYCG.MSA.Mask.20261008 are rebuilt from the same v8.2 masks.
getMask(), listAvailableMasks() and backgroundMask() read the newest KYCG.platform.Mask.date sesameData lists. They used to search every listed version, whose tracks share names, so which build a track came from depended on listing order. A track name only an older build has is still found there. backgroundMask() for HM450/EPIC therefore now uses M_nonuniq and the M_1baseSwitchSNPcommon tracks, as SeSAMe2 does.

Fixed readControls() building the control data.frame by positional assumption. It named the columns with colnames(ctl) <- c('G','R','col', 'type') over a frame whose signal matrix has four columns, so Color_Channel and Type were cbind-ed past the end of that name vector and arrived unnamed, while ‘type' silently took a signal column. Downstream, controls(sdf)$Type was a vector of integers, so negControls()’s grep("negative", ...) matched nothing and detectionPnegEcdf() failed in ecdf() with "'x' must have 1 or more non-missing values" on EPIC and HM450 -- the platforms whose controls arrive through readControls() rather than as SigDF rows. The columns are now named explicitly.
qualityMask() gained 'platform' and 'mask' arguments, so a custom or combined-array mask can be supplied directly instead of being applied as a separate addMask() step after the fact.

Removed the Google Analytics tag from the vignette header. Vignette rendering no longer contacts an external host at build time, and installed vignettes no longer load a remote tracking script.
Documented sesame-cli, a standalone C implementation of the SeSAMe preprocessing workflow (IDAT to betas, QC, differential methylation, copy number) for large cohorts and pipeline deployment. Its betas agree with this package to within ~1e-3 worst case; the intentional divergences are documented in the sesame-cli NUMERICS.md. This package remains the reference implementation. See the README and https://zwdzwd.github.io/sesame-cli.