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 1.8.0 Index]