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)

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