normalizationFactors {OUTRIDER}R Documentation

Accessor functions for the normalization factors in an OutriderDataSet object.

Description

To normalize raw count data normalization factors can be provided as a matrix. When running controlForConfounders the normalization factors are stored within the OutriderDataset object. This normalization factors are then used to compute the normalized counts.

Usage

## S4 method for signature 'OutriderDataSet'
normalizationFactors(object)

## S4 replacement method for signature 'OutriderDataSet,matrix'
normalizationFactors(object) <- value

## S4 replacement method for signature 'OutriderDataSet,DataFrame'
normalizationFactors(object) <- value

## S4 replacement method for signature 'OutriderDataSet,data.frame'
normalizationFactors(object) <- value

## S4 replacement method for signature 'OutriderDataSet,'NULL''
normalizationFactors(object) <- value

Arguments

object

An OutriderDataSet object.

value

The matrix of normalization factors

Value

A numeric matrix containing the normalization factors or the OutriderDataSet object with an updated normalizationFactors assay.

See Also

DESeq2::normalizationFactors

sizeFactors

Examples


ods <- makeExampleOutriderDataSet()

normFactors <- matrix(runif(nrow(ods)*ncol(ods),0.5,1.5),
    ncol=ncol(ods),nrow=nrow(ods))

# the normalization factors matrix should not have 0's in it
# it should have geometric mean near 1 for each row
normFactorsRM <- normFactors / exp(rowMeans(log(normFactors)))
normalizationFactors(ods) <- normFactorsRM
normalizationFactors(ods)[1:10,1:10]

normalizationFactors(ods) <- NULL
ods <- estimateSizeFactors(ods)
normalizationFactors(ods) <- normFactors
all(normalizationFactors(ods) == t(sizeFactors(ods) * t(normFactors)))


[Package OUTRIDER version 1.4.2 Index]