runDEAnalysis: Perform differential expression analysis on SCE with...

In singleCellTK: Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data

Description

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

Usage

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

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 <- runDEAnalysis(inSCE = sce, groupName1 = "Sample1", method = "DESeq2",
 groupName2 = "Sample2", index1 = 1:20, index2 = 21:40,
 analysisName = "DESeq2")

singleCellTK documentation built on Nov. 8, 2020, 5:21 p.m.