dispersion {DSS} | R Documentation

## Acessor functions for the 'dispersion' slot in a SeqCountData object.

### Description

Dispersion parameter for a gene represents its coefficient of variation of expressions. It characterizes the biological variations.

### Usage

    ## S4 method for signature 'SeqCountSet'
    dispersion(object)
    ## S4 replacement method for signature 'SeqCountSet,numeric'
    dispersion(object) <- value

### Arguments

`object` | A SeqCountData object.
`value` | A numeric vector with the same length as number of genes.

### Details

If the counts from biological replicates are modeled as negative binomial distribution, the variance (v) and mean (m) should hold following relationship: v=m+m^2*phi, where phi is the dispersion. Another interpretation is that phi represents the biological variations among replicates when underlying expressions are modeled as a Gamma distribution.

### Author(s)

Hao Wu <hao.wu@emory.edu>

### See Also

normalizationFactor

### Examples

    data(seqData)
    ## obtain
    seqData=estNormFactors(seqData, "quantile")
    seqData=estDispersion(seqData)
    dispersion(seqData)

    ## assign
    dispersion(seqData)=rep(0.1, nrow(exprs(seqData)))

[Package DSS version 2.38.0 Index]