Classes for type safety.

Description

The CTSS class represents CAGE transcription start sites (CTSS) at single-nucleotide resolution, using GPos as base class. It is used internally by CAGEr for type safety.

The ConsensusClusters class represents consensus clusters. It is used internally by CAGEr for type safety.

Details

The genomeName element of the metadata slot is used to store the name of the BSgenome package used when constructing the CAGEr object. Be careful that calling the CTSS constructor twice in a row will erase the fist metadata (because the GPos constructor does so). CAGEr uses the UnstitchedGPos implementation of GPos.

The CTSS.chr class represents a CTSS object that is guaranteed to be only on a single chromosome. It is used internally by CAGEr for type safety.

Consensus clusters must not overlap, so that a single TSS in the genome can only be attributed to a single cluster.

The TagClusters class represents tag clusters. It is used internally by CAGEr for type safety.

Author(s)

Charles Plessy

Examples

ctss <- CAGEr:::.CTSS( CTSScoordinatesGR(exampleCAGEexp)
                     , bsgenomeName = genomeName(exampleCAGEexp))
genomeName(ctss)

ctss.chr <- as(CTSScoordinatesGR(exampleCAGEexp), "CTSS.chr")