IsoDataSet-getters {NBSplice} | R Documentation |
Obtain information about IsoDataSet slots, according to the given function call.
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)
object |
IsoDataSet class object. |
CPM |
Logical indicating if expression matrix at the isoform level should be in CPM scale. |
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. |
see full example in IsoDataSet-class
Gabriela A. Merino merino.gabriela33@gmail.com and Elmer A. Fernandez efernandez@bdmg.com.ar
## 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)