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 1.38.0 Index]