sizeFactors: SizeFactors accessor and estimation function

In gagneurlab/OUTRIDER: OUTRIDER - OUTlier in RNA-Seq fInDER

SizeFactors accessor and estimation function

Description

Accessor functions for the 'sizeFactors' information in a OutriderDataSet object.

Usage

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

## S4 replacement method for signature 'OutriderDataSet,numeric'
sizeFactors(object) <- value

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

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

Arguments

object	OutriderDataSet
value	A numberic vector of sizeFactors

Details

The estimation of the size factors can also make use of the existing log geometric means in the object. Those can be loaded from an existing model.

Value

An OutriderDatasSet with the estimated sizeFactors, or with the getter function it returns a numeric vector containing the sizeFactors.

See Also

estimateSizeFactors

Examples

ods <- makeExampleOutriderDataSet()
ods <- estimateSizeFactors(ods)
head(sizeFactors(ods))

sizeFactors(ods) <- runif(dim(ods)[2], 0.5, 1.5)
sizeFactors(ods)
counts(ods, normalized=TRUE)[1:10,1:10]
        

gagneurlab/OUTRIDER documentation built on April 29, 2024, 2:22 a.m.