Power_Disc: Run DE analysis by using MAST. Here we output two result...

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

Description

Run DE analysis by using MAST. Here we output two result tables corresponding to two forms of DE genes. These parameters include four gene-wise parameters and two cell-wise parameters.

Usage

Power_Disc(
  DErslt,
  simData,
  alpha = 0.1,
  delta = 0.1,
  strata = seq(0, 1, by = 0.2)
)

Arguments

DErslt	is from the DE analysis by MAST
simData	is the corresponding simulated scRNA-seq dataset (SingCellExperiment)
alpha	is the cutoff for the fdr which can be modified
delta	or the zero ratio change is the cutoff (=0.1) used to determined the high DE genes for Form II
strata	can be modified by the user. By default, it is (0, 0.2], (0.2, 0.4], (0.4, 0.6], (0.6, 0.8], (0.8, 1]

Value

a list of metrics for power analysis such as: stratified targeted power and marginal power.

Examples

data("es_mef_sce")
sce = es_mef_sce[, colData(es_mef_sce)$cellTypes == "fibro"]
set.seed(123)
rix = sample(1:nrow(sce), 500)
sce = sce[rix, ]
estParas = Est2Phase(sce)
simData = Simulate2SCE(n=1000, estParas1 = estParas, estParas2 = estParas)
DErslt = runDE(simData$sce)
Disc_pow = Power_Disc(DErslt, simData)

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