qlfInterest {IntEREst} | R Documentation

## quasi-likelihood F-test

### Description

Compute quasi-likelihood F-test using `edgeR` package. For more information see `glmQLFit` and `glmQLFTest` functions in `edgeR` package.

### Usage

    	qlfInterest(x, design=c(), silent=TRUE, disp="common",
    		coef=c(), contrast=NULL,
    		poisson.bound=TRUE, ...)

### Arguments

`x` | Object of type `SummarizedExperiment`.
`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 `glmQLFTest` for more information.
`contrast` | Numeric vector or matrix specifying contrasts of the linear model coefficients to be tested equal to zero. See `glmQLFTest` for more information.
`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 `glmQLFTest` function in the `edgeR` package.

### Value

All values produced by `glmQLFTest` plus the following :

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

### Author(s)

Ali Oghabian

### See Also

`exactTestInterest`, `glmInterest`, `treatInterest`

### Examples

    #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

[Package IntEREst version 1.16.0 Index]