IsoDataSet-class: IsoDataSet S4 class implementation in R
In NBSplice: Negative Binomial Models to detect Differential Splicing

Description Slots Features Functions Author(s) See Also Examples

This S4 class represents a data set containing isoforms expresion in R.

counts: Matrix containing expression values at the isoform level
geneCounts: Matrix with expression values at the gene level
colData: Data.frame with experiment information. Its rows should be the columns of the counts data.frame
isoGeneRel: Data.frame specifying the isoform-gene relationship
design: Formula to be used in the GLM fit and tests
lowExpIndex: Numeric indicating the positions of low expressed isoforms

Discover differential modifications in the splicing patterns.
Detect and quantify isoform relative expression changes.
Combine the results of both gene and isoform levels analysis.

IsoDataSet S4 class includes the following functions:

initialize: Constructor of IsoDataSet objects.
isoCounts: Get the counts slot.
geneCounts: Get the geneCounts slot.
isoGeneRel: Get the isoGeneRel slot.
colData: Get the colData slot.
designFormula: Get the design slot.
lowExpIndex: Get the lowExpIdx slot.
setDesign: Set the design slot.
buildLowExpIdx: Build the index to identify low expressed isoforms.
NBTest: Perform differential expression analysis.

Gabriela A. Merino merino.gabriela33@gmail.com and Elmer A. Fernandez efernandez@bdmg.com.ar

Other IsoDataSet: IsoDataSet, NBTest, buildData, buildLowExpIdx, designMatrix, geneIso, initialize, isoCountsData, myIsoDataSet

## Data loading
data(isoCounts, package="NBSplice")
data(designMatrix, package="NBSplice")
data(geneIso, package="NBSplice")

## Arguments definition
colName<-"condition"

## Constructor calling
myIsoDataSet<-IsoDataSet(isoCounts, designMatrix, colName, geneIso)

## Identificating Low expressed Isoforms
myIsoDataSet<-buildLowExpIdx(myIsoDataSet)

##Arguments definition
colName<-"condition"
test<-"F"

## Differential splicing test
myDSResults<-NBTest(myIsoDataSet, colName, test)