SeSAMe Supporting Data Package

Bugs

Bug reports are appreciated. Register issues at the SeSAMe issue tracker

About

See SeSAMe: reducing artifactual detection of DNA methylation by Infinium BeadChips in genomic deletions for more details.

Exported functions (user-facing)

Data access and caching:

• sesameDataList() list available data titles
• sesameDataHas() check if titles exist
• sesameDataGet() load a data object by title
• sesameDataCache() / sesameDataCacheAll() cache data locally
• sesameDataGet_resetEnv() clear the in-memory cache

Platform and genome helpers:

• inferPlatformFromProbeIDs() infer platform from probe IDs
• sesameData_check_platform() validate or infer platform
• sesameData_check_genome() validate or infer genome build
• sesameData_getGenomeInfo() load genome metadata

Manifests, probes, and annotation:

• sesameData_getManifestGRanges() load manifest GRanges
• sesameData_getProbesByRegion() select probes by genomic range
• sesameData_getProbesByGene() select probes by gene/promoter
• sesameData_annoProbes() annotate probes by features

Transcript utilities:

• sesameData_getTxnGRanges() get transcripts or merged genes
• sesameData_txnToGeneGRanges() merge transcripts to genes