subsetByBidirectionality: Subset by sample-wise bidirectionality of clusters.

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

Description

A convenient wrapper around calcBidirectionality and subset.

Usage

subsetByBidirectionality(object, ...)

## S4 method for signature 'GRanges'
subsetByBidirectionality(
  object,
  samples,
  inputAssay = "counts",
  outputColumn = "bidirectionality",
  minSamples = 0
)

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

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

Arguments

object	GRanges or RangedSummarizedExperiment: Unstranded clusters with peaks 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.
minSamples	integer: Only regions with bidirectionality above this value are retained.

Value

object with bidirectionality values added as a column, and low bidirectionaly regions removed.

See Also

Other Subsetting functions: subsetByComposition(), subsetBySupport()

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

Examples

data(exampleCTSSs)
data(exampleBidirectional)

# Keep only clusters that are bidirectional in at least one sample:
subsetByBidirectionality(exampleBidirectional, samples=exampleCTSSs)

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