DTA.generate {DTA} | R Documentation

## Simulation of DTA experiments

### Description

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

### Usage

    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)

### Arguments

`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.

### Value

DTA.generate returns a list, containing the following entries

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

### Author(s)

Bjoern Schwalb schwalb@lmb.uni-muenchen.de

### References

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.

### Examples

    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)

[Package DTA version 2.28.0 Index]