CTSS-class {CAGEr} | R Documentation |
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.
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.
Charles Plessy
ctss <- CAGEr:::.CTSS( CTSScoordinatesGR(exampleCAGEexp) , bsgenomeName = genomeName(exampleCAGEexp)) genomeName(ctss) ctss.chr <- as(CTSScoordinatesGR(exampleCAGEexp), "CTSS.chr")