Description Usage Arguments Details Value Examples

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

1 2 | ```
## S4 method for signature 'DEXSeqDataSet'
estimateDispersions( object, fitType=c("parametric","local","mean"), maxit=100, niter=10, quiet=FALSE, formula=design(object), BPPARAM=SerialParam())
``` |

`object` |
A DEXSeqDataSet |

`fitType` |
Either "parametric", "local", or "mean" for the type of fitting of dispersions to the mean intensity. See ?estimateDispersions,DESeqDataSet-method for details. |

`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.

1 2 3 | ```
data(pasillaDEXSeqDataSet, package="pasilla")
dxd <- estimateSizeFactors( dxd )
dxd <- estimateDispersions( dxd )
``` |

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