estimateDispersions_BM {DEXSeq}R Documentation

Estimate exon dispersions, using the deprecated "big model" method

Description

This function estimates for each counting bin of the ExonCountSet object a dispersion value. It stores these values in fData(ecs)$dispersionBeforeSharing.

Usage

estimateDispersions_BM( object,
         formula=count ~ sample + condition * exon,
         initialGuess=.01, nCores=1, minCount=10,
         maxExon=70, quiet=FALSE, file="")

Arguments

object

An ExonCountSet object.

formula

Formula used in the GLM to estimate the dispersion values. The terms in the formula must be design columns of the ExonCountSet object, the l.h.s. must be count.

initialGuess

An initial guess for the dispersion values to initiate the optimization.

nCores

Number of cores to be used to estimate the dispersions. The parallel package must be loaded in order to spread the job onto several cores.

minCount

Counting bins with less than minCount counts (summed over all samples) are skipped in the tests. This reduces computation time, as counting bins with very few counts cannot give a significant signal anyway. For skipped counting bins, the testable column in fData is set to FALSE.

maxExon

Genes with more than maxExon counting bins will be skipped in the test. This option can be useful when otherwise genes with very many counting bins use up extremely long computation time for dispersion estimation and testing for differential exon usage.

quiet

If TRUE, no progress report is shown. In case the session is not an interactive session and a progress report is wanted, include a file name in the parameter file.

file

A file name to write the progress reports. If file is "", the output will be written to the standard output connection.

Details

For the dispersion estimation, we use the Cox-Reid conditional maximum likelihood method of Gordon Smyth et al., which they devised for the edgeR package.

Value

An object of class ExonCountSet with dispersion featureData(object)$dispersion_CR_est) parameters filled).

Examples

if(suppressWarnings(require("pasilla", quietly=TRUE, character.only=TRUE))){

   data("pasillaExons", package="pasilla")
   pasillaExons <- estimateSizeFactors( pasillaExons )
   pasillaExons <- estimateDispersions( pasillaExons )

}
[Package DEXSeq version 1.8.0 Index]