IsoDataSet-class {NBSplice} | R Documentation |
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:
Constructor of IsoDataSet objects.
Get the counts slot.
Get the geneCounts slot.
Get the isoGeneRel slot.
Get the colData slot.
Get the design slot.
Get the lowExpIdx slot.
Set the design slot.
Build the index to identify low expressed isoforms.
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)