runDEAnalysis {singleCellTK} | R Documentation

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

### Description

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

### Usage

    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")

[Package singleCellTK version 2.2.0 Index]