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`, `tagClusters`

### Examples

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

[Package CAGEr version 1.30.3 Index]