Perform differential expression analysis on SCE with specified method Method supported: 'MAST', 'DESeq2', 'Limma', 'ANOVA'

runDEAnalysis(method = c("MAST", "DESeq2", "Limma", "ANOVA", "wilcox"), ...)

Arguments

method	A single character for specific method. Choose from `"MAST"`, `"DESeq2"`, `"Limma"`, `"ANOVA"`. Default `"MAST"`.
...	Other arguments passed to specific functions. Refer to `runMAST`, `runDESeq2`, `runLimmaDE`, `runANOVA`

Value

Input SCE object with metadata(inSCE) updated with name "diffExp" as a list object. Detail refers to the four child functions.

Examples

data(scExample, package = "singleCellTK")
sce <- subsetSCECols(sce, colData = "type != 'EmptyDroplet'")
sce <- scaterlogNormCounts(sce, "logcounts")
sce <- runDEAnalysis(inSCE = sce, groupName1 = "Sample1", method = "wilcox",
 groupName2 = "Sample2", index1 = seq(20), index2 = seq(21,40),
 analysisName = "Limma")