# Generate synthetic count data sets

### Description

Generate synthetic count data sets, following the simulation strategy detailed in Soneson and Delorenzi (2013).

### Usage

1 2 3 4 5 6 7 8 | ```
generateSyntheticData(dataset, n.vars, samples.per.cond, n.diffexp,
repl.id = 1, seqdepth = 1e+07, minfact = 0.7, maxfact = 1.4,
relmeans = "auto", dispersions = "auto", fraction.upregulated = 1,
between.group.diffdisp = FALSE, filter.threshold.total = 1,
filter.threshold.mediancpm = 0, fraction.non.overdispersed = 0,
random.outlier.high.prob = 0, random.outlier.low.prob = 0,
single.outlier.high.prob = 0, single.outlier.low.prob = 0,
effect.size = 1.5, output.file = NULL)
``` |

### Arguments

`dataset` |
A name or identifier for the data set/simulation settings. |

`n.vars` |
The initial number of genes in the simulated data set. Based on the filtering conditions ( |

`samples.per.cond` |
The number of samples in each of the two conditions. |

`n.diffexp` |
The number of genes simulated to be differentially expressed between the two conditions. |

`repl.id` |
A replicate ID for the specific simulation instance. Useful for example when generating multiple count matrices with the same simulation settings. |

`seqdepth` |
The base sequencing depth (total number of mapped reads). This number is multiplied by a value drawn uniformly between |

`minfact,maxfact` |
The minimum and maximum for the uniform distribution used to generate factors that are multiplied with |

`relmeans` |
A vector of mean values to use in the simulation of data from the Negative Binomial distribution, or |

`dispersions` |
A vector or matrix of dispersions to use in the simulation of data from the Negative Binomial distribution, or |

`fraction.upregulated` |
The fraction of the differentially expressed genes that is upregulated in condition 2 compared to condition 1. |

`between.group.diffdisp` |
Whether or not the dispersion should be allowed to be different between the conditions. Only applicable if |

`filter.threshold.total` |
The filter threshold on the total count for a gene across all samples. All genes for which the total count across all samples is less than the threshold will be filtered out. |

`filter.threshold.mediancpm` |
The filter threshold on the median count per million (cpm) for a gene across all samples. All genes for which the median cpm across all samples is less than the threshold will be filtered out. |

`fraction.non.overdispersed` |
The fraction of the genes that should be simulated according to a Poisson distribution, without overdispersion. The non-overdispersed genes will be divided proportionally between the upregulated, downregulated and non-differentially expressed genes. |

`random.outlier.high.prob` |
The fraction of 'random' outliers with unusually high counts. |

`random.outlier.low.prob` |
The fraction of 'random' outliers with unusually low counts. |

`single.outlier.high.prob` |
The fraction of 'single' outliers with unusually high counts. |

`single.outlier.low.prob` |
The fraction of 'single' outliers with unusually low counts. |

`effect.size` |
The strength of the differential expression, i.e., the effect size, between the two conditions. If this is a single number, the effect sizes will be obtained by simulating numbers from an exponential distribution (with rate 1) and adding the results to the |

`output.file` |
If not |

### Details

In the comparison function, only results obtained for data sets with the same value of the `dataset`

parameter will be compared. Hence, it is important to give the same value of this parameter e.g. to different replicates generated with the same simulation settings.

For more detailed information regarding the different types of outliers, see Soneson and Delorenzi (2013).

Mean and dispersion parameters (if `relmeans`

and/or `dispersions`

is set to `"auto"`

) are sampled from values estimated from the data sets by Pickrell et al (2010) and Cheung et al (2010). The data sets were downloaded from the ReCount web page (Frazee et al (2011)) and processed as detailed by Soneson and Delorenzi (2013).

To get the actual mean value for the Negative Binomial distribution used for the simulation of counts for a given sample, take the column `truemeans.S1`

(or `truemeans.S2`

, if the sample is in condition S2) of the `variable.annotations`

slot, divide by the sum of the same column and multiply with the base sequencing depth (provided in the `info.parameters`

list) and the depth factor for the sample (given in the `sample.annotations`

data frame). Thus, if you have a vector of mean values that you want to provide as the `relmeans`

argument and make sure to use it 'as-is' in the simulation (for condition S1), make sure to set the `seqdepth`

argument to the sum of the values in the `relmeans`

vector, and to set `minfact`

and `maxfact`

equal to 1.

### Value

A `compData`

object. If `output.file`

is not `NULL`

, the object is saved in the given `output.file`

(which should have an `.rds`

extension).

### Author(s)

Charlotte Soneson

### References

Soneson C and Delorenzi M (2013): A comparison of methods for differential expression analysis of RNA-seq data. BMC Bioinformatics 14:91

Cheung VG, Nayak RR, Wang IX, Elwyn S, Cousins SM, Morley M and Spielman RS (2010): Polymorphic cis- and trans-regulation of human gene expression. PLoS Biology 8(9):e1000480

Frazee AC, Langmead B and Leek JT (2011): ReCount: a multi-experiment resource of analysis-ready RNA-seq gene count datasets. BMC Bioinformatics 12:449

Pickrell JK, Marioni JC, Pai AA, Degner JF, Engelhardt BE, Nkadori E, Veyrieras JB, Stephens M, Gilad Y and Pritchard JK (2010): Understanding mechanisms underlying human gene expression variation with RNA sequencing. Nature 464, 768-772

Robles JA, Qureshi SE, Stephen SJ, Wilson SR, Burden CJ and Taylor JM (2012): Efficient experimental design and analysis strategies for the detection of differential expression using RNA-sequencing. BMC Genomics 13:484

### Examples

1 2 | ```
mydata.obj <- generateSyntheticData(dataset = "mydata", n.vars = 1000,
samples.per.cond = 5, n.diffexp = 100)
``` |

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