SimulateMultiSCEs: Simulate the data for multiple-group comparisons; e.g.,...

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

Description

Simulate the data for multiple-group comparisons; e.g., different cell types in blood It simulates the DE changes in two forms corresponding two types of DE genes

Usage

SimulateMultiSCEs(
  n = 1000,
  estParas_set,
  multiProb,
  delta1 = 0.1,
  delta2 = 0.5
)

Arguments

n	the number of total cells for multiple groups; e.g., 1000, 2000, and etc.
estParas_set	a set of parameters corresponding to different cell types.
multiProb	a vector of probilities correponding to each cell type. It is not necessary to sum up to 1 because POWSC will normalize internally.
delta1	the minimum of expression change used to determine the Form I DE.
delta2	the minimum of log fold change used to determine the Form II DE.

Value

a list of simulated datasets. Each dataset corresponds to a pair-wise comparison including a series of metrics such as the DE gene indices for Form I and II DE genes, and simulated expression data in singlecellexperiment format.

Examples

data("es_mef_sce")
set.seed(123)
rix = sample(1:nrow(es_mef_sce), 500)
es_mef_sce = es_mef_sce[rix, ]
sce1 = es_mef_sce[, colData(es_mef_sce)$cellTypes == "fibro"]
estParas1 = Est2Phase(sce1)
sce2 = es_mef_sce[, colData(es_mef_sce)$cellTypes == "stemCell"]
estParas2 = Est2Phase(sce2)
estParas_set = list(celltype1 = estParas1, celltype2 = estParas1, celltype3 =estParas2)
multiProb = c(0.2, 0.3, 0.5)
simData = SimulateMultiSCEs(n=200, estParas_set = estParas_set, multiProb = multiProb)

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