normFactors: Accessors for the 'normFactors' slot of an srnadiffExp object

In mzytnicki/srnadiff: Finding differentially expressed unannotated genomic regions from RNA-seq data

Accessors for the 'normFactors' slot of an srnadiffExp object

Description

The normFactors slot holds the normalization factors as a named vector with sample names.

Usage

## S4 method for signature 'srnadiffExp'
normFactors(object)

## S4 replacement method for signature 'srnadiffExp,numeric'
normFactors(object) <- value

Arguments

object	An srnadiffExp object.
value	A numeric vector, one size factor for each sample in the coverage data.

Details

The normFactors vector assigns to each sample coverage a value, the normalization factor, such that count values in each sample coverage can be brought to a common scale by dividing by the corresponding normalization factor. This step is also called normalization, its purpose is to render coverages (counts) from different samples, which may have been sequenced to different depths, comparable. Normalization factors are estimated using the median ratio method described by Equation 5 in Anders and Huber (2010). Alternative normalization factor estimators can also be supplied using the assignment function sizeFactors<-.

Value

The normalization factors, in a list.

References

Simon Anders, and Wolfgang Huber (2010). Differential expression analysis for sequence count data. Genome Biology, 11:106.

Examples

srnaExp <- srnadiffExample()
normFactors(srnaExp)

mzytnicki/srnadiff documentation built on March 7, 2023, 2:18 a.m.