EventPointer {EventPointer} | R Documentation |
Statistical analysis of alternative splcing events
EventPointer( Design, Contrast, ExFit, Eventstxt, Filter = TRUE, Qn = 0.25, Statistic = "LogFC", PSI = FALSE )
Design |
The design matrix for the experiment. |
Contrast |
The contrast matrix for the experiment. |
ExFit |
aroma.affymetrix pre-processed variable after using
|
Eventstxt |
Path to the EventsFound.txt file generated by CDFfromGTF function. |
Filter |
Boolean variable to indicate if an expression filter is applied |
Qn |
Quantile used to filter the events (Bounded between 0-1, Q1 would be 0.25). |
Statistic |
Statistical test to identify differential splicing events, must be one of : LogFC, Dif_LogFC or DRS. |
PSI |
Boolean variable to indicate if Delta PSI should be calculated for every splicing event. |
Data.frame ordered by the splicing p.value . The object contains the different information for each splicing event such as Gene name, event type, genomic position, p.value, z.value and delta PSI.
data(ArraysData) Dmatrix<-matrix(c(1,1,1,1,0,0,1,1),nrow=4,ncol=2,byrow=FALSE) Cmatrix<-t(t(c(0,1))) EventsFound<-paste(system.file('extdata',package='EventPointer'),'/EventsFound.txt',sep='') Events<-EventPointer(Design=Dmatrix, Contrast=Cmatrix, ExFit=ArraysData, Eventstxt=EventsFound, Filter=TRUE, Qn=0.25, Statistic='LogFC', PSI=TRUE)