glmInterest: generalized linear model likelihood ratio tests
In IntEREst: Intron-Exon Retention Estimator

Description Usage Arguments Value Author(s) See Also Examples

Compute generalized linear model likelihood ratio tests using edgeR package. For more information see glmfit and glmLRT() functions in edgeR package.

1 2	glmInterest(x, design=c(), silent=TRUE, disp="common", coef=c(), contrast=NULL, ...)

`x`	Object of type `SummarizedExperiment`.
`design`	Design matrix.
`silent`	Whether run the function silently, i.e. without printing the top differential expression tags. 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 `glmLRT()` in `edgeR` for more information.
`contrast`	Numeric vector or matrix specifying contrasts of the linear model coefficients to be tested equal to zero. See `glmLRT()` in `edgeR` for more information.
`...`	Other parameter settings for the `glmLRT()` function in the `edgeR` package.

All values produced by glmLRT in edgeR package plus following:

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

Ali Oghabian

exactTestInterest, qlfInterest, treatInterest

#Test retention differentiation across the 3 types of sampels
group <- getAnnotation(mdsChr22Obj)[,"type"]
glmRes<- glmInterest(x=mdsChr22Obj, 
	design=model.matrix(~group), silent=TRUE, 
	disp="tagwiseInitTrended", coef=2:3, contrast=NULL)