calcTPM {CAGEfightR} | R Documentation

## Calculate CAGE Tags-Per-Million (TPM)

### Description

Normalize CAGE-tag counts into TPM values.

### Usage

    calcTPM(
      object,
      inputAssay = "counts",
      outputAssay = "TPM",
      totalTags = NULL,
      outputColumn = "totalTags"
    )

### Arguments

`object` | RangedSummarizedExperiment: CAGE data quantified at CTSS, cluster or gene-level.
`inputAssay` | character: Name of assay holding input expression values.
`outputAssay` | character: Name of assay to hold TPM values.
`totalTags` | character or NULL: Column in colData holding the total number of tags for each samples. If NULL, this will be calculated using calcTotalTags.
`outputColumn` | character: Name of column in colData to hold number of total tags, only used if totalTags is NULL.

### Value

object with TPM-values added as a new assay. If totalTags is NULL, total tags added as a column in colData.

### See Also

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

### Examples

    data(exampleUnidirectional)

    # Calculate TPM:
    calcTPM(exampleUnidirectional)

    # Use pre-calculated total number of tags:
    calcTPM(exampleUnidirectional,
            outputAssay='TPMsupplied',
            totalTags='totalTags')

[Package CAGEfightR version 1.7.5 Index]