Description Usage Arguments Value Author(s) See Also Examples
View source: R/srcLineagePulse_simulateDataSet.R
Set either vecGeneWiseDropoutRates or matDropoutModelExternal.
1 2 3 4 | 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.
1 2 3 4 5 6 7 8 9 10 11 | 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,])
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