simRNAseq {PROPER} | R Documentation

## Simulate RNA-seq count data

### Description

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.

### Usage

    simRNAseq(simOptions, n1, n2)

### Arguments

`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.

### Details

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

### Value

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.

### Author(s)

Hao Wu <hao.wu@emory.edu>

### See Also

RNAseq.SimOptions.2grp, runSims

### Examples

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

[Package PROPER version 1.18.0 Index]