subsetBySupport: Subset by support across samples

Description Usage Arguments Value See Also Examples

View source: R/subsetBy.R

Description

A convienient wrapper around calcSupport and subset.

Usage

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subsetBySupport(
  object,
  inputAssay = "counts",
  outputColumn = "support",
  unexpressed = 0,
  minSamples = 1
)

Arguments

object

RangedSummarizedExperiment: CAGE data quantified at CTSS, cluster or gene-level.

inputAssay

character: Name of assay holding input expression values.

outputColumn

character: Name of column in rowRanges to hold support values.

unexpressed

numeric: Support will be calculated based on features larger than this cutoff.

minSamples

numeric: Only features with support in more than this number of samples will be kept.

Value

RangedSummarizedExperiment with support added as a column in rowRanges and features with less support than minSamples removed.

See Also

Other Subsetting functions: subsetByBidirectionality(), subsetByComposition()

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

Examples

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data(exampleBidirectional)

# Keep clusters with at least one tag in two samples
subsetBySupport(exampleBidirectional)

# Keep clusters with at least two tags in four samples
subsetBySupport(exampleBidirectional, unexpressed=1, minSamples=2)

CAGEfightR documentation built on Nov. 8, 2020, 5:42 p.m.