simulateContinuousDataSet: Simulate a data set for LinagePulse Simulates a data set with...

In YosefLab/LineagePulse: Differential expression analysis and model fitting for single-cell RNA-seq data

Description

Set either vecGeneWiseDropoutRates or matDropoutModelExternal.

Usage

simulateContinuousDataSet(scaNCells, scaNConst, scaNLin, scaNImp,
  scaMumax = 100, scaSDMuAmplitude = 1, vecNormConstExternal = NULL,
  vecDispExternal = NULL, vecGeneWiseDropoutRates = NULL,
  matDropoutModelExternal = NULL)

Arguments

scaNCells	(scalar) Number of cells in data set.
scaNConst	(scalar) Number of constant expression profiles (genes) in data set.
scaNLin	(scalar) Number of linear expression profiles (genes) in data set.
scaNImp	(scalar) Number of impulse model expression profiles (genes) in data set.
scaMumax	(scalar) [Default 1000] Maximum expression mean parameter to be used.
scaSDMuAmplitude	(scalar) [Default 1] Standard deviation of normal distribution form which the amplitude change within an impulse trace is drawn.
vecNormConstExternal	(numeric vector number of cells) [Default NULL] Size factors for data set. Size factors are set to 1 if this is not specified (NULL).
vecDispExternal	(numeric vector number of genes) [Default NULL] Dispersion parameters per gene supplied by user.s
vecGeneWiseDropoutRates	(numeric vector number of cells) [Default NULL] One drop-out rate per gene.
matDropoutModelExternal	(numeric matrix cells x 2) [Default NULL] External drop-out model, has to have one row for each simulated cell.

Value

list (length 2)

• continuous (numerical vector length number of cells) Continuous covariates (1D) of cells. One scalar per cell. This covariate could be pseudotime for example.'

• counts (matrix genes x cells) Sampled count data of all cells after drop-out.

Author(s)

David Sebastian Fischer

See Also

Called by separately by user.

Examples

lsSimulatedData <- simulateContinuousDataSet(
    scaNCells = 100,
    scaNConst = 10,
    scaNLin = 10,
    scaNImp = 10,
    scaMumax = 100,
    scaSDMuAmplitude = 3,
    vecNormConstExternal=NULL,
    vecDispExternal=rep(20, 30),
    vecGeneWiseDropoutRates = rep(0.1, 30))
plot(lsSimulatedData$annot$continuous, lsSimulatedData$counts[1,])

YosefLab/LineagePulse documentation built on May 6, 2019, 2:19 p.m.