calcBidirectionality {CAGEfightR} | R Documentation

## Calculate sample-wise bidirectionally of clusters.

### Description

For each cluster, calculate how many individual samples shows transcription in both directions. This is refered to as the 'bidirectionality'. Clusters must be unstranded (*) and have a midpoint stored in the thick column

### Usage

    calcBidirectionality(object, ...)

    ## S4 method for signature 'GRanges'
    calcBidirectionality(
      object,
      samples,
      inputAssay = "counts",
      outputColumn = "bidirectionality"
    )

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

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

### Arguments

`object` | GenomicRanges or RangedSummarizedExperiment: Unstranded clusters with midpoints stored in the 'thick' column.
`...` | additional arguments passed to methods.
`samples` | RangedSummarizedExperiment: Sample-wise CTSSs stored as an assay.
`inputAssay` | character: Name of assay in samples holding input CTSS values.
`outputColumn` | character: Name of column in object to hold bidirectionality values.

### Value

object returned with bidirectionality scores added in rowData (or mcols).

### See Also

Other Calculation functions: `calcComposition()`, `calcPooled()`, `calcShape()`, `calcSupport()`, `calcTPM()`, `calcTotalTags()`, `subsetByBidirectionality()`, `subsetByComposition()`, `subsetBySupport()`

### Examples

    data(exampleCTSSs)
    data(exampleBidirectional)

    calcBidirectionality(exampleBidirectional, samples=exampleCTSSs)

[Package CAGEfightR version 1.10.0 Index]