Description Usage Arguments Details Value

Simulate RNA-seq counts from the cell-assign model

1 2 3 4 5 6 7 8 9 10 11 12 | ```
simulate_cellassign(
rho,
s,
pi,
delta,
B = 20,
a,
beta,
X = NULL,
min_Y = 0,
max_Y = 1000
)
``` |

`rho` |
A gene by cell type binary matrix relating markers to cell types |

`s` |
A vector of cell-specific size factors |

`pi` |
An ordinal vector relating each cell to its true marker type assignment |

`delta` |
Gene by cell type matrix delta (all entries with corresponding zeros in rho will be ignored) |

`B` |
Granularity of spline-based fitting of dispersions |

`a` |
Alpha parameters for spline inference of dispersions |

`beta` |
A gene by covariate vector of coefficients - the first column should correspond to the intercept (baseline expression) values |

`X` |
A cell by covariate matrix of covariates - the intercept column will always be added. |

`b` |
Beta parameters for spline inference of dispersions |

The number of genes, cells, and cell types is automatically inferred from the dimensions of rho (gene by cell-type) and s (vector of length number of cells). The specification of X is optional - a column of ones will always be added as an intercept.

An N by G matrix of simulated counts

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