calcTPM: Calculate CAGE Tags-Per-Million (TPM)

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

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')

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