subsetBySupport: Subset by support across samples

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

Description

A convienient wrapper around calcSupport and subset.

Usage

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

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)

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