runDE: A wrapper function for calling DE genes. This contains two...

In suke18/POWSC: Simulation, power evaluation, and sample size recommendation for single cell RNA-seq

Description

A wrapper function for calling DE genes. This contains two methods: MAST and SC2P

Usage

runDE(sce, DE_Method = c("MAST", "SC2P"))

Arguments

sce	is a simulated scRNA-seq dataset with two-group conditions, e.g., treatment vs control.
DE_Method	is a string chosen from "MAST" or "SC2P".

Value

a list of three tables: the first table summaries the DE result for both forms of DE genes. cont table represents the result for continous case. disc table shows the result for discontinous case.

Examples

data("es_mef_sce")
sce = es_mef_sce[, colData(es_mef_sce)$cellTypes == "fibro"]
set.seed(123)
rix = sample(1:nrow(sce), 500)
sce = sce[rix, ]
estParas = Est2Phase(sce)
simData = Simulate2SCE(n=100, estParas1 = estParas, estParas2 = estParas)
sim_sce = simData$sce
DErslt = runDE(sim_sce)

suke18/POWSC documentation built on April 2, 2021, 4:34 a.m.