estimateExonDispersionsForModelFrame {DEXSeq}R Documentation

Estimates exon dispersions

Description

This function calculates the individual dispersions for each counting bins for a single gene. It takes as input a model frame generated from the function modelFrameForGene.

Usage

estimateExonDispersionsForModelFrame(modelFrame, formula=NULL, mm=NULL, 
                                                 muhat=NULL, initialGuess=0.01)

Arguments

modelFrame

Model frame provided by the function modelFrameForGene.

formula

Formula for the glm used to estimate the dispersions. The factors in the formula must be present in the column names of the model frame. If it is left NULL, the default formula used is "count ~ sample + condition * exon".

mm

A model matrix for the model frame. If NULL, a model matrix will be created from the parameters "formula" and "modelFrame".

muhat

Initial values for the coefficients in the optimization. If NULL, initial values will be calculated using with the dispersion value given by the parameter "initialGuess".

initialGuess

An initial guess of the dispersions to initiate the optimization.

Value

A vector of exon dispersions.

See Also

estimateDispersions

Examples

	data("pasillaExons", package="pasilla")
	pasillaExons <- estimateSizeFactors( pasillaExons )
	estimateExonDispersionsForModelFrame(modelFrameForGene(pasillaExons, "FBgn0085442"))

[Package DEXSeq version 1.0.2 Index]