subsetBySupport {CAGEfightR} | R Documentation

## Subset by support across samples

### 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)

[Package CAGEfightR version 1.10.0 Index]