Description Usage Arguments Value Author(s) See Also Examples

Compute quasi-likelihood F-test using `edgeR`

package. For more
information see `glmQLFit`

and `glmQLFTest`

functions
in `edgeR`

package.

1 2 3 |

`x` |
Object of type |

`design` |
Design matrix. |

`silent` |
Whether run silently, i.e. without printing the top differential expression tags. The default is TRUE. |

`disp` |
The method of estimating the dispersion in the data. Available options are: "common", "trended", "tagwiseInitCommon" and "tagwiseInitTrended". It is also possible to assign a number. |

`coef` |
Integer or character vector indicating which coefficients of the linear model
are to be tested equal to zero. See |

`contrast` |
Numeric vector or matrix specifying contrasts of the linear model coefficients
to be tested equal to zero. See |

`poisson.bound` |
Logical value, if TRUE (i.e. default) the pvalue would be higher than when obtained fom likelihood ratio test while Negative Binomial dispersion is zero. |

`...` |
Other parameter settings for the |

All values produced by `glmQLFTest`

plus the following :

`dispersionType` |
The name of the type of dispersion used. |

`dispersion` |
The estimated dispersion values. |

Ali Oghabian

`exactTestInterest`

, `glmInterest`

,
`treatInterest`

1 2 3 4 5 6 7 | ```
#Test retention differentiation across the 3 types of sampels
group <- getAnnotation(mdsChr22Obj)[,"type"]
qlfRes<- qlfInterest(x=mdsChr22Obj,
design=model.matrix(~group), silent=TRUE,
disp="tagwiseInitTrended", coef=2:3, contrast=NULL)
qlfRes
``` |

IntEREst documentation built on Dec. 4, 2018, 6:02 p.m.

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