SCRIPsimu: SCRIP simulation

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

SCRIP simulation

Description

Simulate count data for single cell RNA-sequencing using SCIRP method

Usage

SCRIPsimu(
  data,
  params,
  method = "single",
  base_allcellmeans_SC = NULL,
  pre.bcv.df = NULL,
  libsize = NULL,
  bcv.shrink = 1,
  Dropout_rate = NULL,
  mode = "GP-trendedBCV",
  de.prob = NULL,
  de.downProb = NULL,
  de.facLoc = NULL,
  de.facScale = NULL,
  path.skew = NULL,
  batch.facLoc = NULL,
  batch.facScale = NULL,
  path.nSteps = NULL,
  ...
)

Arguments

data	data matrix required to fit the mean-BCV trend for simulation
params	SplatParams object containing parameters for the simulation
method	"single", "groups" or "paths"
base_allcellmeans_SC	base mean vector provided to help setting DE analysis
pre.bcv.df	BCV.df enables us to change the variation of BCV values
libsize	library size can be provided directly
bcv.shrink	factor to control the BCV levels
Dropout_rate	factor to control the dropout rate directly
mode	"GP-commonBCV", "BP-commonBCV", "BP", "BGP-commonBCV" and "BGP-trendedBCV"
de.prob	the proportion of DE genes
de.downProb	the proportion of down-regulated DE genes
de.facLoc	DE location factor
de.facScale	DE scale factor
path.skew	Controls how likely cells are from the start or end point of the path
batch.facLoc	DE location factor in batch
batch.facScale	DE scale factor in batch
path.nSteps	number of steps between the start point and end point for each path
...	Other parameters

Value

SingleCellExperiment file

Examples

data(params_acinar)
data(acinar.data)
sim_trend = SCRIPsimu(data=acinar.data, params=params_acinar, mode="GP-trendedBCV")

thecailab/SCRIP documentation built on March 1, 2023, 7:56 p.m.