estimateSizeFactors {DEXSeq} | R Documentation

## Estimate the size factors for a DEXSeqDataSet

### Description

Estimate the size factors for a DEXSeqDataSet

### Usage

      ## S4 method for signature 'DEXSeqDataSet'
    estimateSizeFactors(object,locfunc=median,geoMeans)

### Arguments

`object` | a DEXSeqDataSet
`locfunc` | a function to compute a location for a sample. By default, the median is used. However, especially for low counts, the `shorth` function from the genefilter package may give better results.
`geoMeans` | by default this is not provided and the geometric means of the counts are calculated within the function. A vector of geometric means from another count matrix can be provided for a "frozen" size factor calculation

### Details

This function calls the method estimateSizeFactors for the DESeqDataSet object, and adapts it to the specific use to the DEXSeqDataSet.

### Value

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

### References

- Simon Anders, Wolfgang Huber: Differential expression analysis for sequence count data. Genome Biology 11 (2010) R106, http://dx.doi.org/10.1186/gb-2010-11-10-r106

[Package DEXSeq version 1.40.0 Index]