subsetByBidirectionality: Subset by sample-wise bidirectionality of clusters.

Description Usage Arguments Value See Also Examples

Description

A convenient wrapper around calcBidirectionality and subset.

Usage

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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

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data(exampleCTSSs)
data(exampleBidirectional)

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

MalteThodberg/CAGEfightR documentation built on Oct. 24, 2018, 12:10 p.m.