testForDEU {DEXSeq} | R Documentation |
This function tests for differential exon usage for each of
the genes in the object. It stores the results in the fields
fData(ecs)$pvalue
and fData(ecs)$padjust
.
testForDEU(ecs, formula0=NULL, formula1=NULL, nCores=1, quiet=FALSE, file="")
ecs |
An ExonCountSet object. |
formula0 |
Formula for the null model to be used in the GLM fit. If no formula
is given, the default |
formula1 |
Formula for the full model to be used in the GLM fit. If no formula
is given, the default |
nCores |
Number of CPUcores to be used to estimate the dispersions.
The |
quiet |
If TRUE, no progress report is shown. In case the session is not an interactive session and progress report is wanted. Change the name of the file. |
file |
A file name to write the progress reports. If file="", output will be written in the standard output connection. |
The terms in the formulas must be columns of design(ecs)
. In addition,
in formula1
, the variable exonID
is set to the
ID of the currently tested exon counting bin.
See testGeneForDEU
, which is called for each gene, for further details.
An ExonCountSet object with fData(ecs)$pvalue
and
fData(ecs)$padjust
data slots filled.
estimateExonDispersionsForModelFrame
## Not run: data("pasillaExons", package="pasilla") pasillaExons <- estimateSizeFactors( pasillaExons ) pasillaExons <- estimateDispersions( pasillaExons ) pasillaExons <- fitDispersionFunction( pasillaExons ) pasillaExons <- testForDEU( pasillaExons ) ## End(Not run)