calcBidirectionality: Calculate sample-wise bidirectionally of clusters.

Description Usage Arguments Value See Also Examples

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

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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

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