calcPooled: Calculate pooled expression across all samples.

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

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)

CAGEfightR documentation built on Nov. 8, 2020, 5:42 p.m.