estimatelog2FoldChanges {DEXSeq}R Documentation

Fold changes (log2) from the fitted expression values in the GLM.

Description

This function calculates the fold changes (on log2 scale) between the different conditions. It calculates them from the coefficients of a GLM that fits the read counts to a variable of the experimental design specified by the user (see below, parameter "fitExpToVar").

Usage

estimatelog2FoldChanges(ecs, fitExpToVar="condition", 
          denominator="", getOnlyEffects=FALSE, averageOutExpression=TRUE, 
          nCores=1, quiet=FALSE, file="")

Arguments

ecs

An ExonCountSet object.

fitExpToVar

A variable contained in design(ecs). The expression values will be fitted to this variable using the the formula "count ~ sample + fitExpToVar * exon".

denominator

A value of the sample annotation (e.g. condition) to use as a denominator in the log2 fold change. As a default, the function will take the annotation of the first sample

getOnlyEffects

If TRUE, the raw effects are added as columns to the feature data and any operation (log2) is performed with them.

averageOutExpression

The default, TRUE, gives back splicing effects. If FALSE, the gene expression effects won't be substracted.

nCores

Number of CPU cores to be used to estimate the dispersions. The multicore package need to be loaded beforehands to parallelize over several cores.

quiet

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

file

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

Examples

     ## Not run: 
         data("pasillaExons", package="pasilla")
         pasillaExons <- estimateSizeFactors( pasillaExons )
         pasillaExons <- estimateDispersions( pasillaExons )
         pasillaExons <- fitDispersionFunction( pasillaExons ) 
         pasillaExons <- estimatelog2FoldChanges( pasillaExons )
     
## End(Not run)
[Package DEXSeq version 1.8.0 Index]