Description Usage Arguments Details Value Note References See Also Examples

Simulate data arising from multiple independent RNA-seq experiments

1 | ```
sim.function(param, dispFuncs, nrep = 4, classes = NULL, inter.sd = 0.3)
``` |

`param` |
Mean expression levels: |

`dispFuncs` |
List of length equal to the number of studies to be simulated, containing the gamma regression parameters describing the mean-dispersion relationship for each one; these are the mean-dispersion functions linking mean and intra-study variability for each independent experiment. |

`nrep` |
Number of replicates to be simulated in each condition in each study. Ignored if |

`classes` |
List of class memberships, one per study (maximum 20 studies). Each vector or factor of the list can only
contain two levels which correspond to the two conditions studied. If NULL, |

`inter.sd` |
Inter-study variability. By default, |

Details about the simulation procedure are given in the following paper:

A matrix with simulated expression levels, one row per gene and one column per replicate. Names of studies are given in the column names of the matrix.

If the `param`

data provided in this package are not used to simulate data, one should check that the
per-condition means in `param`

are reasonable. Note also that for genes to be simulated as non-differentially
expressed, the values of "mucond1" and "mucond2" in `param`

should be equal.

A. Rau, G. Marot and F. Jaffrezic (2014). Differential meta-analysis of RNA-seq data. *BMC Bioinformatics* **15**:91

1 2 3 4 5 6 7 8 9 10 11 12 13 | ```
## Load simulation parameters
data(param)
data(dispFuncs)
## Simulate data
matsim <- sim.function(param = param, dispFuncs = dispFuncs)
sim.conds <- colnames(matsim)
rownames(matsim) <-paste("tag", 1:dim(matsim)[1],sep="")
# extract simulated data from one study
simstudy1 <- extractfromsim(matsim,"study1")
head(simstudy1$study)
simstudy1$pheno
``` |

```
rep1 rep2 rep3 rep4 rep5 rep6 rep7 rep8
tag1 489 584 411 621 510 473 387 728
tag2 760 697 858 1000 756 520 814 951
tag3 134 66 184 130 147 146 75 118
tag4 288 259 164 250 501 590 389 1025
tag5 0 4 3 1 6 0 3 7
tag6 125 134 16 21 24 30 31 33
study condition
rep1 study1 untreated
rep2 study1 untreated
rep3 study1 untreated
rep4 study1 untreated
rep5 study1 treated
rep6 study1 treated
rep7 study1 treated
rep8 study1 treated
```

metaRNASeq documentation built on May 29, 2017, 2:53 p.m.

Embedding an R snippet on your website

Add the following code to your website.

For more information on customizing the embed code, read Embedding Snippets.