normFactors {srnadiff} | R Documentation

## 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)

[Package srnadiff version 1.11.0 Index]