CTSS-class {CAGEr} | R Documentation

## 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")

[Package CAGEr version 1.28.0 Index]