calcPooled {CAGEfightR} | R Documentation

## Calculate pooled expression across all samples.

### Description

Sum expression of features across all samples to obtain a 'pooled' signal.

### Usage

    calcPooled(object, inputAssay = "TPM", outputColumn = "score")

### 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 pooled expression.

### Value

object with pooled expression added as a column in rowRanges.

### See Also

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

### Examples

    data(exampleCTSSs)

    # Calculate TPM using supplied total number of tags:
    exampleCTSSs <- calcTPM(exampleCTSSs, totalTags='totalTags')

    # Sum TPM values over samples:
    calcPooled(exampleCTSSs)

[Package CAGEfightR version 1.10.0 Index]