IsoDataSet-getters: Getters for an IsoDataSet object.

In NBSplice: Negative Binomial Models to detect Differential Splicing

Description

Obtain information about IsoDataSet slots, according to the given function call.

Usage

isoCounts(object, CPM = TRUE)

## S4 method for signature 'IsoDataSet'
isoCounts(object, CPM = TRUE)

geneCounts(object)

## S4 method for signature 'IsoDataSet'
geneCounts(object)

isoGeneRel(object)

## S4 method for signature 'IsoDataSet'
isoGeneRel(object)

expData(object)

## S4 method for signature 'IsoDataSet'
expData(object)

designFormula(object)

## S4 method for signature 'IsoDataSet'
designFormula(object)

lowExpIndex(object)

## S4 method for signature 'IsoDataSet'
lowExpIndex(object)

Arguments

object	IsoDataSet class object.
CPM	Logical indicating if expression matrix at the isoform level should be in CPM scale.

Value

According to the call one of the following objects can be returned

matrix	Isoform expression matrix.
matrix	Gene expression matrix.
data.frame	Experiment information.
data.frame	Isoforms-gene relationships.
formula	Formula to be used in the GLM fit.
numeric	Index of low expressed isoforms.

Note

see full example in IsoDataSet-class

Author(s)

Gabriela A. Merino [e-mail] and Elmer A. Fernandez [e-mail]

See Also

IsoDataSet

Examples

## Data loading
data(myIsoDataSet, package="NBSplice")

## Getting isoform expression counts
myCounts<-isoCounts(myIsoDataSet)
head(myCounts)
## Data loading
data(myIsoDataSet, package="NBSplice")

## Getting gene expression counts
myGeneCounts<-geneCounts(myIsoDataSet)
head(myGeneCounts)
## Data loading
data(myIsoDataSet, package="NBSplice")

## Getting isoform-gene relationships
myIsoGeneRel<-isoGeneRel(myIsoDataSet)
head(myIsoGeneRel)
## Data loading
data(myIsoDataSet, package="NBSplice")

## Getting the design matrix
myDesignMatrix<-expData(myIsoDataSet)
myDesignMatrix
## Data loading
data(myIsoDataSet, package="NBSplice")

## Getting the model formula
myFormula<-designFormula(myIsoDataSet)
myFormula
## Data loading
data(myIsoDataSet, package="NBSplice")

## Getting index of low expressed isoforms
myLowExpIdx<-lowExpIndex(myIsoDataSet)
head(myLowExpIdx)

NBSplice documentation built on Nov. 8, 2020, 8:07 p.m.