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 1.13.1 Index]