Description Usage Arguments Value References

Simulation for Differential Proportion Case

1 2 | ```
simuDP(Dataset1, Simulated_Data, DEIndex, samplename, Zeropercent_Base, f, FC,
coeff, RP, modeFC, DP, generateZero, constantZero, varInflation)
``` |

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

`Simulated_Data` |
Required input empty matrix to provide structure information of output matrix with simulated data |

`DEIndex` |
Index for DE genes |

`samplename` |
The name for genes that chosen for simulation |

`Zeropercent_Base` |
Zero percentage for corresponding gene expression values |

`f` |
Fold change values (number of SDs) for each gene |

`FC` |
Fold Change values for DE Simulation |

`coeff` |
Relationship coefficients for Mean and Variance |

`RP` |
matrix for NB parameters for genes in samplename |

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

`DP` |
Differetial Proportion vector |

`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 Simulated dataset for DP

Korthauer KD, Chu LF, Newton MA, Li Y, Thomson J, Stewart R, Kendziorski C. A statistical approach for identifying differential distributions in single-cell RNA-seq experiments. Genome Biology. 2016 Oct 25;17(1):222. https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-1077-y

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