distclu: Distance clustering

In charles-plessy/CAGEr: Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data for precise mapping of transcription start sites and promoterome mining

Distance clustering

Description

The "distclu" method is an implementation of simple distance-based clustering of data attached to sequences, where two neighbouring TSSs are joined together if they are closer than some specified distance (see GenomicRanges::reduce for implementation details.

Usage

distclu(object, maxDist = 20, keepSingletonsAbove = 0)

## S4 method for signature 'SummarizedExperiment'
distclu(object, maxDist = 20, keepSingletonsAbove = 0)

## S4 method for signature 'CTSS'
distclu(object, maxDist = 20, keepSingletonsAbove = 0)

## S4 method for signature 'CAGEexp'
distclu(object, maxDist = 20, keepSingletonsAbove = 0)

Arguments

object	The SummarizedExperiment::RangedSummarizedExperiment object containing CTSS information, or just a CTSS object.
maxDist	Maximal distance between two neighbouring CTSSs for them to be part of the same cluster.
keepSingletonsAbove	Remove "singleton" tag clusters of width 1 with signal ⁠< keepSingletonsAbove⁠. Default value 0 results in keeping all TCs by default. Setting it to Inf removes all singletons.

Details

Clustering is done for every CAGE dataset within the CAGEr object separately, resulting in a different set of tag clusters for every CAGE dataset. TCs from different datasets can further be aggregated into a single referent set of consensus clusters by calling the aggregateTagClusters function.

Value

For CTSS input, a TagClusters object, for SummarizedExperiment input, a GRangesList of TagClusters objects, and for CAGEexp input, a modified object containing the tag clusters stored as a GRangesList of TagClusters objects in its metadata slot tagClusters.

Author(s)

Vanja Haberle

Charles Plessy

See Also

aggregateTagClusters

Other CAGEr clustering methods: consensusClustersTpm(), paraclu()

Other CAGEr object modifiers: CTSStoGenes(), CustomConsensusClusters(), aggregateTagClusters(), annotateCTSS(), cumulativeCTSSdistribution(), getCTSS(), normalizeTagCount(), paraclu(), quantilePositions(), quickEnhancers(), resetCAGEexp(), summariseChrExpr()

Other CAGEr clusters functions: CTSScumulativesTagClusters(), CustomConsensusClusters(), aggregateTagClusters(), consensusClustersDESeq2(), consensusClustersGR(), cumulativeCTSSdistribution(), paraclu(), plotInterquantileWidth(), quantilePositions(), tagClustersGR()

Examples

distclu(CTSSnormalizedTpmGR(exampleCAGEexp, 1)[1:10])
distclu(CTSStagCountSE(exampleCAGEexp)[1:25,])
ce <- distclu(exampleCAGEexp, maxDist = 20, keepSingletonsAbove = 100)
tagClustersGR(ce, "Zf.30p.dome")

charles-plessy/CAGEr documentation built on Aug. 2, 2024, 4:35 p.m.