Description Usage Arguments Value Author(s) References Examples

DTA.generate produces the phenotype matrix and the matrix containing the simulated data according to the given parameters.

1 | ```
DTA.generate(timepoints, tnumber = NULL, plabel = NULL, nrgenes = 5000, mediantime = 12, ccl = 150, delaytime = 0, sdnoise = 0.075, nobias = FALSE, unspecific.LtoU = 0, unspec.LtoU.weighted = FALSE, unspecific.UtoL = 0, unspec.UtoL.weighted = FALSE, truehalflives = NULL, truecomplete = NULL, genenames = NULL, cDTA = FALSE)
``` |

`timepoints` |
Integer vector containing the labeling times for which the samples should be generated. |

`tnumber` |
Integer vector containing the number of uridine residues for each gene. If NULL, tnumber is sampled from an F-distribution within the function. |

`plabel` |
The labeling efficiency. If NULL, plabel is set to 0.005 within the function. For details, see supplemental material of Sun et al. (see references). |

`nrgenes` |
The number of genes the simulated experiment will have (will be cropped if it exceeds the length of tnumber). |

`mediantime` |
The median of the randomly drawn half-life distribution. |

`ccl` |
The cell cycle length (in minutes). |

`delaytime` |
Estimates the delay between the moment of 4sU/4tU labeling and actual incorporation of it into mRNA. |

`sdnoise` |
The amount of measurement noise (proportional to expression strength). |

`nobias` |
Should a labeling bias be added? |

`unspecific.LtoU` |
Proportion of labeled RNAs that unspecifically end up in the unlabeled fraction. |

`unspec.LtoU.weighted` |
Should unspecific proportion of labeled to unlabeled depend linearly on the length of the RNA? |

`unspecific.UtoL` |
Proportion of unlabeled RNAs that unspecifically end up in the labeled fraction. |

`unspec.UtoL.weighted` |
Should unspecific proportion of unlabeled to labeled depend linearly on the length of the RNA? |

`truehalflives` |
If the data should be generated using a given half-life distribution, this vector must contain the respective values for each gene. |

`truecomplete` |
If the data should be generated using a given expression distribution, this vector must contain the respective values for each gene. |

`genenames` |
An optional list of gene names. |

`cDTA` |
cDTA = FALSE does not rescale L and U. |

DTA.generate returns a list, containing the following entries

`phenomat` |
A matrix, containing the design of the experiment as produced by |

`datamat` |
A matrix, containing the simulated measurements from U, L and T, according to the design given in phenomat. |

`tnumber` |
Integer vector containing the number of uridine residues for each gene. |

`ccl` |
The cell cycle length (in minutes). |

`truecomplete` |
A vector, containing the true amount of total RNA. |

`truelambdas` |
A vector, containing the true decay rates. |

`truemus` |
A vector, containing the true synthesis rates. |

`truehalflives` |
A vector, containing the true half-lives. |

`trueplabel` |
The true labeling efficiency. For details, see supplemental material of Miller et al. (see references). |

`truear` |
The true parameter ar. For details, see supplemental material of Miller et al. (see references). |

`truebr` |
The true parameter br. For details, see supplemental material of Miller et al. (see references). |

`truecr` |
The true parameter cr. For details, see supplemental material of Miller et al. (see references). |

`truecrbyar` |
The true parameter cr/ar. For details, see supplemental material of Miller et al. (see references). |

`truecrbybr` |
The true parameter cr/br. For details, see supplemental material of Miller et al. (see references). |

`truebrbyar` |
The true parameter br/ar. For details, see supplemental material of Miller et al. (see references). |

`trueLasymptote` |
The true parameter asymptote (labeled bias). For details, see supplemental material of Miller et al. (see references). |

`trueUasymptote` |
The true parameter asymptote (unlabeled bias). For details, see supplemental material of Miller et al. (see references). |

Bjoern Schwalb [email protected]

C. Miller, B. Schwalb, K. Maier, D. Schulz, S. Duemcke, B. Zacher, A. Mayer, J. Sydow, L. Marcinowski, L. Doelken, D. E. Martin, A. Tresch, and P. Cramer. Dynamic transcriptome analysis measures rates of mRNA synthesis and decay in yeast. Mol Syst Biol, 7:458, 2011. M. Sun, B. Schwalb, D. Schulz, N. Pirkl, L. Lariviere, K. Maier, A. Tresch, P. Cramer. Mutual feedback between mRNA synthesis and degradation buffers transcript levels in a eukaryote. Under review. B. Schwalb, B. Zacher, S. Duemcke, D. Martin, P. Cramer, A. Tresch. Measurement of genome-wide RNA synthesis and decay rates with Dynamic Transcriptome Analysis (DTA/cDTA). Bioinformatics.

1 2 3 4 5 | ```
sim.object = DTA.generate(timepoints=rep(c(6,12),2))
### for control plots set 'check = TRUE' ###
res.sim = DTA.estimate(ratiomethod = "bias",simulation = TRUE,sim.object = sim.object,check = FALSE)
``` |

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