Description Usage Arguments Value

View source: R/Single_Cell_Simu.R

Called by `simulateSet`

to simulate a specified number of genes
from
one DD category at a time.

1 2 3 4 | ```
singleCellSimu(Dataset1, Method, index, FC, modeFC, DP, Validation = FALSE,
numGenes = 1000, numDE = 100, numSamples = 100,
generateZero = c("empirical", "simulated", "constant"),
constantZero = NULL, varInflation = NULL)
``` |

`Dataset1` |
Numeric matrix of expression values with genes in rows and samples in columns. |

`Method` |
Type of simulation should choose from "DE" "DP" "DM" "DB" |

`index` |
Reasonable set of genes for simulation |

`FC` |
Fold Change values for DE Simulation |

`modeFC` |
Vector of values to use for fold changes between modes for DP, DM, and DB. |

`DP` |
Differetial Proportion vector |

`Validation` |
Show Validation plots or not |

`numGenes` |
numeric value for the number of genes to simulate |

`numDE` |
numeric value for the number of genes that will differ between two conditions |

`numSamples` |
numeric value for the number of samples in each condition to simulate |

`generateZero` |
Specification of how to generate the zero values.
If " |

`constantZero` |
Numeric value between 0 and 1 that indicates the fixed
proportion of zeroes for every gene.
Ignored if |

`varInflation` |
Optional numeric vector with one element for each condition that corresponds to the multiplicative variance inflation factor to use when simulating data. Useful for sensitivity studies to assess the impact of confounding effects on differential variance across conditions. Currently assumes all samples within a condition are subject to the same variance inflation factor. |

Simulated_Data A list object where the first element contains a matrix of the simulated dataset, the second element contains the DEIndex, and the third element contains the fold change (between two conditions for DE, between two modes for DP, DM, and DB).

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