Description Usage Arguments Details Value Author(s) See Also Examples

This function generate simulated RNA-seq count data for a two-group comparison design. It takes an object for simulation option (return object from 'RNAseq.SimOptions.2grp' function, and sample sizes (replicates in each condition, then generate a matrix of counts.

1 | ```
simRNAseq(simOptions, n1, n2)
``` |

`simOptions` |
An object for simulation option. This should be the return object from 'RNAseq.SimOptions.2grp' function. |

`n1, n2` |
Sample size in two treatment groups. |

The count data are generated based a negative binomial (NB) distribution. Parameters for NB are provided in the input object.

A list with following fields:

`counts` |
A matrix of dimension ngenes x (n1+n2). Each row is for a gene, each column is for a sample. Columns 1 to n1 are for the first condition. The rest columns are for the other condition. |

`designs` |
A vector/matrix representing the experimental designs. In a two-group comparison, it's a simple 0/1 vector. |

`DEid` |
The ID (row index) for true DE genes. |

`simOptions` |
The simulation option object. This is exactly the same as the input simOptions. |

Hao Wu <hao.wu@emory.edu>

RNAseq.SimOptions.2grp, runSims

1 2 3 | ```
simOptions = RNAseq.SimOptions.2grp()
data = simRNAseq(simOptions, n1=3, n2=3)
names(data)
``` |

```
[1] "counts" "designs" "DEid" "simOptions"
```

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