swapScores: Swap scores in SummarizedExperiment

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

Description

Take scores for a specific sample and a specific assay and put them into rowData.

Usage

swapScores(object, outputColumn = "score", inputAssay, sample)

Arguments

object	SummarizedExperiment: CAGE-data
outputColumn	character: Column in rowData to to hold swapped in scores.
inputAssay	character: Name of assay to take scores from.
sample	character: Name of sample to take scores from.

Value

SummarizedExperiment with sample scores from inputAssay in rowRata.

See Also

Other Swapping functions: swapRanges()

Examples

data(exampleCTSSs)
sample_names <- colnames(exampleCTSSs)

# Replace scores with values from the first sample:
x <- swapScores(exampleCTSSs, inputAssay='counts', sample=sample_names[1])
rowRanges(x)

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