SeSAMe is an R package for processing Infinium DNA methylation data. SeSAMe currently supports EPICv2, EPIC, HM450, HM27, MSA, MM285 and Mammal40 platforms and dynamically generated manifest.
To install from Github,
BiocManager::install("zwdzwd/sesame")
See the package Home Page on Bioconductor and the Developmental Branch.
It also has a depended data package for annotation and example data.
SeSAMe comes as two implementations that share the same methods and are developed together. They are parallel, not sequential — neither is an upgrade of the other, and the version lines say which is which:
sesame (this package) — SeSAMe v1, on the 1.x series. The reference implementation of the SeSAMe methods and the interactive R toolkit for exploratory analysis and KYCG enrichment. Actively maintained on Bioconductor, and the oracle the C version is validated against. This package stays on 1.x.
BiocManager::install("sesame")
SeSAMe2 — the second implementation, on the 2.x series: a standalone C program (no R, no Bioconductor, no network) covering the full workflow — IDAT → betas → QC → differential methylation → copy number → SNP genotyping, with visualization through cinderplot. Built for large cohorts, pipeline deployment, and non-R environments.
conda install -c zhou-lab -c conda-forge sesame yame
Both installables are called sesame, because they are one project and one
method. They never meet in a resolver: BiocManager reads Bioconductor's
index, conda reads the zhou-lab channel. So sesame 2.0.0 from conda is not a
newer version of sesame 1.31.x from Bioconductor — it is the other
implementation.
R is SeSAMe2's permanent oracle, and the agreement is gated on every release.
Raw betas (prep="") are bit-identical; across the full default pipeline,
probes with identical raw input agree to a median of ~6e-6 and ~1e-3 worst
case. Every intentional numerical divergence is recorded in SeSAMe2's
NUMERICS.md, and
the few places where the two answer genuinely different questions — all of them
annotation-lineage differences, none a tolerance — in
DIVERGENCES.md.
Bug reports are appreciated. Register issues at the SeSAMe issue tracker.
Please cite and reference SeSAMe: reducing artifactual detection of DNA methylation by Infinium BeadChips in genomic deletions for more details.