simulateContinuousDataSet {LineagePulse} | R Documentation |
Set either vecGeneWiseDropoutRates or matDropoutModelExternal.
simulateContinuousDataSet(scaNCells, scaNConst, scaNLin, scaNImp, scaMumax = 100, scaSDMuAmplitude = 1, vecNormConstExternal = NULL, vecDispExternal = NULL, vecGeneWiseDropoutRates = NULL, matDropoutModelExternal = NULL)
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. |
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.
David Sebastian Fischer
Called by separately by user.
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,])