calcPooled: Calculate pooled expression across all samples.

Description Usage Arguments Value See Also Examples

View source: R/calc.R

Description

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

Usage

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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

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data(exampleCTSSs)

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

# Sum TPM values over samples:
calcPooled(exampleCTSSs)

MalteThodberg/CAGEfightR documentation built on Oct. 24, 2018, 12:10 p.m.