estimateSizeFactors {DESeq}R Documentation

Estimate the size factors for a CountDataSet

Description

Estimate the size factors for a CountDataSet

Usage

## S4 method for signature 'CountDataSet'
estimateSizeFactors( object, locfunc=median, ... )

Arguments

object

a CountDataSet

locfunc

a function to compute a location for a sample. By default, the median is used. However, especially for low counts, the shorth may give better results.

...

extra arguments are ignored

Details

You need to call this function right after newCountDataSet unless you have manually specified size factors.

Typically, the function is called with the idiom

cds <- estimateSizeFactors( cds )

This estimates the size factors and stores the information in the object.

Internally, the function calls estimateSizeFactorsForMatrix. See there for more details on the calculation.

Value

The CountDataSet passed as parameters, with the size factors filled in.

Author(s)

Simon Anders, sanders@fs.tum.de

See Also

estimateSizeFactorsForMatrix

Examples

cds <- makeExampleCountDataSet()
cds <- estimateSizeFactors( cds )
sizeFactors( cds )

[Package DESeq version 1.6.1 Index]