qlfInterest: quasi-likelihood F-test

In gacatag/IntEREst: Intron-Exon Retention Estimator

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

gacatag/IntEREst documentation built on Aug. 20, 2023, 6:06 p.m.