Description Usage Arguments Value Author(s) See Also Examples

This function fits negative binomial GLMs to reduced models defined either by the "contrast" parameter, or by one or several model coefficients (specified by "coef" parameter) set to zero. Subsequently, a likelihood ratio test is applied, to identify windows significantly dependent on the tested coefficient.

1 2 |

`qs` |
a qseaSet object |

`glm` |
a qseaGLM object |

`contrast` |
numeric vector specifying a contrast of the model coefficients. This contrast can for example be defined using limma::makeContrasts() |

`coef` |
alternatively defines the contrast by coefficient(s) of the model tested to be equal to zero. |

`name` |
short descriptive name for the contrast (as "TvsN"), used for examples in columns of result tables |

`verbose` |
more messages that document the process |

`nChunks` |
fit GLMs in multiple chunks |

`parallel` |
use multicore processing |

This function returns the qseaGLM object, extended by the fitted coefficients of the reduced GLMs, as well as the test statistics. Note that one qseaGLM object can contain several contrasts.

Mathias Lienhard

limma::makeContrasts(), fitNBglm(), isSignificant()

1 2 3 4 | ```
qs=getExampleQseaSet()
design=model.matrix(~group, getSampleTable(qs))
TvN_glm=fitNBglm(qs, design, norm_method="beta")
TvN_glm=addContrast(qs,TvN_glm, coef=2, name="TvN")
``` |

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