estimateDispersions | R Documentation |

This function obtains dispersion estimates for negative binomial distributed data for the specific case for DEXSeq.

```
## S4 method for signature 'DEXSeqDataSet'
estimateDispersions(
object,
fitType = c("parametric", "local", "mean", "glmGamPoi"),
maxit = 100,
niter = 10,
quiet = FALSE,
formula = design(object),
BPPARAM = SerialParam()
)
```

`object` |
A DEXSeqDataSet. |

`fitType` |
Either "parametric", "local", "mean" or "glmGamPoi" for the type of fitting of dispersions to the mean intensity. See ?estimateDispersions,DESeqDataSet-method for details. If "glmGamPoi" is selected, the GLM fitter from "glmGamPoi" is also used for estimating the dispersion estimates. |

`maxit` |
Control parameter: maximum number of iterations to allow for convergence |

`niter` |
Number of times to iterate between estimation of means and estimation of dispersion. |

`quiet` |
Whether to print messages at each step. |

`formula` |
Formula used to fit the dispersion estimates. |

`BPPARAM` |
A "BiocParallelParam" instance. See |

See ?estimateDispersions,DESeqDataSet-method for details.

A DEXSeqDataSet with the dispersion information filled in as metadata columns.

```
data(pasillaDEXSeqDataSet, package="pasilla")
dxd <- estimateSizeFactors( dxd )
dxd <- estimateDispersions( dxd )
```

Embedding an R snippet on your website

Add the following code to your website.

For more information on customizing the embed code, read Embedding Snippets.