simu_DE {SCRIP}

SCRIP simulation for differential expression

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