CustomConsensusClusters {CAGEr} | R Documentation

## Expression levels of consensus cluster

### Description

Intersects custom consensus clusters with the CTSS data in a `CAGEexp` object, and stores the result as a expression matrices (raw and normalised tag counts).

### Usage

    CustomConsensusClusters(
      object,
      clusters,
      threshold = 0,
      nrPassThreshold = 1,
      thresholdIsTpm = TRUE
    )

    ## S4 method for signature 'CAGEexp,GRanges'
    CustomConsensusClusters(
      object,
      clusters,
      threshold = 0,
      nrPassThreshold = 1,
      thresholdIsTpm = TRUE
    )

### Arguments

`object` | A `CAGEexp` object
`clusters` | Consensus clusters in `GRanges` format.
`threshold, nrPassThreshold` | Only CTSSs with signal `>= threshold` in `>= nrPassThreshold` experiments will be used for clustering and will contribute towards total signal of the cluster.
`thresholdIsTpm` | Logical, is threshold raw tag count value (FALSE) or normalized signal (TRUE).

### Details

Consensus clusters must not overlap, so that a single base of the genome can only be attributed to a single cluster. This is enforced by the `.ConsensusClusters` constructor.

### Value

stores the result as a new `RangedSummarizedExperiment` in the `experiment` slot of the object. The assays of the new experiment are called `counts` and `normalized`. An `outOfClusters` column is added to the sample metadata to reflect the number of molecules that do not have their TSS in a consensus cluster.

### Author(s)

Charles Plessy

### See Also

Other CAGEr object modifiers: `CTSStoGenes()`, `aggregateTagClusters()`, `annotateCTSS()`, `clusterCTSS()`, `cumulativeCTSSdistribution()`, `getCTSS()`, `normalizeTagCount()`, `quantilePositions()`, `summariseChrExpr()`

Other CAGEr clusters functions: `CTSSclusteringMethod()`, `CTSScumulativesTagClusters()`, `aggregateTagClusters()`, `clusterCTSS()`, `consensusClustersDESeq2()`, `consensusClustersGR()`, `cumulativeCTSSdistribution()`, `plotInterquantileWidth()`, `quantilePositions()`, `tagClustersGR()`

### Examples

    cc <- consensusClustersGR(exampleCAGEexp)
    CustomConsensusClusters(exampleCAGEexp, cc)

[Package CAGEr version 2.0.2 Index]