NEWS

sesame 1.31.6

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.