estimateSizeFactors: Estimate the size factors for a DEXSeqDataSet

In areyesq89/DEXSeq: Inference of differential exon usage in RNA-Seq

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

areyesq89/DEXSeq documentation built on Oct. 15, 2023, 1:40 p.m.