treatInterest: Differential retention test relative to a threshold

In gacatag/IntEREst: Intron-Exon Retention Estimator

Differential retention test relative to a threshold

Description

Compute a genewise statistical test relative to a fold-change threshold using edgeR package. For more information see glmTreat function in edgeR package.

Usage

	treatInterest(x, design=c(), silent=TRUE, disp="common", 
		coef=c(), contrast=NULL, lfc=0, ...)

Arguments

x	Object of class SummarizedExperiment.
design	Design matrix.
silent	Whether run 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 glmTreat for more information.
contrast	Numeric vector or matrix specifying contrasts of the linear model coefficients to be tested equal to zero. See glmTreat for more information.
lfc	Numeric scalar i.e. the log fold change threshold.
...	Other parameter settings for the glmFit function in the edgeR package.

Value

All values produced by glmTreat plus the following :

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

Author(s)

Ali Oghabian

See Also

exactTestInterest, qlfInterest, glmInterest

Examples

group <- getAnnotation(mdsChr22Obj)[,"type"]

#Test retention differentiation across the 3 types of sampels 
# The log fold change threshold is 0
treatRes<- treatInterest(x=mdsChr22Obj, 
	design=model.matrix(~group), silent=TRUE, 
	disp="tagwiseInitTrended", coef=2:3, contrast=NULL, lfc=0)
treatRes

gacatag/IntEREst documentation built on July 29, 2024, 1:12 a.m.