qlfInterest: quasi-likelihood F-test
In IntEREst: Intron-Exon Retention Estimator

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.

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

`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.

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

#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