SCRIPsimu {SCRIP}

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")