simu_DE: SCRIP simulation for differential expression

In SCRIP: An Accurate Simulator for Single-Cell RNA Sequencing Data

Description

Simulate count data for differential expression analysis using SCRIP

Usage

simu_DE(
  expre_data,
  params,
  nGenes = NULL,
  nDE,
  ncells = NULL,
  FC,
  Dropout_rate = NULL,
  libsize = NULL,
  pre.bcv.df = NULL,
  bcv.shrink = 1,
  seed = 2021
)

Arguments

expre_data	data matrix required for simulation
params	SplatParams object containing parameters for the simulation
nGenes	number of genes simulated
nDE	number of differentially expressed genes simulated
ncells	number of cells simulated
FC	fold change rate simulated between two groups
Dropout_rate	factor to control the dropout rate directly
libsize	library size used for simulation
pre.bcv.df	BCV.df enables us to change the variation of BCV values
bcv.shrink	factor to control the BCV levels
seed	seed for simulation

Value

SummarizedExperiment files from both groups for DE analysis and DE genes index

SCRIP documentation built on Nov. 19, 2021, 9:07 a.m.