calcBidirectionality: Calculate sample-wise bidirectionally of clusters.

In MalteThodberg/CAGEfightR: Analysis of Cap Analysis of Gene Expression (CAGE) data using Bioconductor

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)

MalteThodberg/CAGEfightR documentation built on Sept. 11, 2021, 4:42 a.m.