runDEAnalysis {singleCellTK} | R Documentation |
Perform differential expression analysis on SCE with specified method Method supported: 'MAST', 'DESeq2', 'Limma', 'ANOVA'
runDEAnalysis(method = c("MAST", "DESeq2", "Limma", "ANOVA"), ...)
method |
A single character for specific method. Choose from
|
... |
Other arguments passed to specific functions. Refer to
|
Input SCE object with metadata(inSCE)
updated with name
"diffExp"
as a list
object. Detail refers to the four child
functions.
data(scExample, package = "singleCellTK") sce <- subsetSCECols(sce, colData = "type != 'EmptyDroplet'") sce <- runDEAnalysis(inSCE = sce, groupName1 = "Sample1", method = "DESeq2", groupName2 = "Sample2", index1 = 1:20, index2 = 21:40, analysisName = "DESeq2")