IsoDataSet S4 class implementation in R

Description

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

Slots

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

Features

1. Discover differential modifications in the splicing patterns.

2. Detect and quantify isoform relative expression changes.

3. Combine the results of both gene and isoform levels analysis.

Functions

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.

Author(s)

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

See Also

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

Examples

## 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)