clusterUnidirectionally {CAGEfightR} | R Documentation

## Unidirectional Clustering (Tag Clustering) of pooled CTSSs.

### Description

Finds unidirectional Tag Clusters (TCs) with a pooled TPM above a certain threshold using a slice-reduce approach. Addtionally calculates the sum and peak position of the TCs.

### Usage

    clusterUnidirectionally(object, ...)

    ## S4 method for signature 'GRanges'
    clusterUnidirectionally(object, pooledCutoff = 0,
      mergeDist = 20L)

    ## S4 method for signature 'RangedSummarizedExperiment'
    clusterUnidirectionally(object, ...)

    ## S4 method for signature 'GPos'
    clusterUnidirectionally(object, ...)

### Arguments

`object` | GRanges or RangedSummarizedExperiment: Basepair-wise pooled CTSS.
`...` | additional arguments passed to methods.
`pooledCutoff` | numeric: Minimum pooled value to be considered as TC.
`mergeDist` | integer: Merge TCs within this distance.

### Value

GRanges with TPM sum as the score column, and TC peak as the thick column.

### See Also

Other Clustering functions: `clusterBidirectionally`, `trimToPeak`, `trimToPercentiles`, `tuneTagClustering`

### Examples

    data(exampleCTSSs)

    # Calculate pooledTPM, using supplied number of total tags
    exampleCTSSs <- calcTPM(exampleCTSSs,
                            inputAssay='counts',
                            outputAssay='TPM',
                            totalTags='totalTags')
    exampleCTSSs <- calcPooled(exampleCTSSs, inputAssay='TPM')

    # Cluster using defaults: slice-threshold of 0 and reduce-distance of 20
    clusterUnidirectionally(exampleCTSSs)

    # Use custom thresholds:
    clusterUnidirectionally(exampleCTSSs, pooledCutoff=1, mergeDist=25)

[Package CAGEfightR version 1.6.0 Index]