DTA.dynamic.generate {DTA} | R Documentation

## Simulation of DTA experiments upon perturbation

### Description

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

### Usage

    DTA.dynamic.generate(duration = 60,lab.duration = 6,tnumber = NULL,plabel = NULL,nrgenes = 5000,mediantime.halflives = 12,mediantime.synthesisrates = 18,n = 1,ccl = NULL,check = TRUE,plots = FALSE,save.plots = FALSE,folder = NULL,condition = "",addformat = NULL,sdnoise = 0.075,nobias = FALSE,unspecific.LtoU = 0,unspec.LtoU.weighted = FALSE,unspecific.UtoL = 0,unspec.UtoL.weighted = FALSE,mu.values.mat = NULL,mu.breaks.mat = NULL,lambda.values.mat = NULL,lambda.breaks.mat = NULL,truehalflives = NULL,truesynthesisrates = NULL,genenames = NULL)

### Arguments

`duration` | duration of the whole time course (min)
`lab.duration` | labeling duration for single experiments (min)
`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.halflives` | the median of the half life distribution
`mediantime.synthesisrates` | the median of the synthesis rates distribution (counts/cell/cellcycle)
`n` | the number of cells N(0)
`ccl` | The cell cycle length (in minutes).
`check` | if check=TRUE, control messages will be generated
`plots` | if plots = TRUE, control plots will be plotted
`save.plots` | if save.plots = TRUE, control plots will be saved
`folder` | folder, where to save the plots
`condition` | to be added to the plotnames
`addformat` | additional fileformat for plots to be saved
`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?
`mu.values.mat` | if the data should be generated using given synthesis rates, this matrix must contain the respective values for each gene
`mu.breaks.mat` | timepoints of synthesis rate changes, this matrix must contain the respective values for each gene, only needed when mu.values.mat is given (one column less than mu.values.mat)
`lambda.values.mat` | if the data should be generated using given decay rates, this matrix must contain the respective values for each gene
`lambda.breaks.mat` | timepoints of decay rate changes, this matrix must contain the respective values for each gene, only needed when lambda.values.mat is given (one column less than lambda.values.mat)
`truehalflives` | If the data should be generated using a given half-life distribution, this vector must contain the respective values for each gene.
`truesynthesisrates` | If the data should be generated using a given synthesis rates distribution, this vector must contain the respective values for each gene
`genenames` | An optional list of gene names.

### Value

DTA.dynamic.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).
`truemus` | A vector, containing the true synthesis rates.
`truemusaveraged` | A vector, containing the true synthesis rates, averaged over the labeling period.
`truelambdas` | A vector, containing the true decay rates.
`truelambdasaveraged` | A vector, containing the true decay rates, averaged over the labeling period.
`truehalflives` | A vector, containing the true half-lives.
`truehalflivesaveraged` | A vector, containing the true half-lives, averaged over the labeling period.
`trueplabel` | The true labeling efficiency. For details, see supplemental material of Sun et al. (see references).
`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. Dolken, 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

    nrgenes = 5000
    truesynthesisrates = rf(nrgenes,5,5)*18
    steady = rep(1,nrgenes)
    shock = 1/pmax(rnorm(nrgenes,mean = 8,sd = 4),1)
    induction = pmax(rnorm(nrgenes,mean = 8,sd = 4),1)
    changes.mat = cbind(steady,shock,shock*induction)
    mu.values.mat = changes.mat*truesynthesisrates
    mu.breaks.mat = cbind(rep(12,nrgenes),rep(18,nrgenes))
    truehalflives = rf(nrgenes,15,15)*12
    truelambdas = log(2)/truehalflives
    changes.mat = cbind(steady,shock,shock*induction,steady)
    lambda.values.mat = changes.mat*truelambdas
    lambda.breaks.mat = cbind(rep(12,nrgenes),rep(18,nrgenes),rep(27,nrgenes))

    ### it takes several min to build sim.object (depends on the number of genes 'nrgenes') ###

    sim.object = DTA.dynamic.generate(duration = 36,lab.duration = 6,nrgenes = nrgenes,mu.values.mat = mu.values.mat,mu.breaks.mat = mu.breaks.mat,lambda.values.mat = lambda.values.mat,lambda.breaks.mat = lambda.breaks.mat)

    ### for control plots set 'check = TRUE' ###

    res = DTA.dynamic.estimate(simulation = TRUE,sim.object = sim.object,check = FALSE)

[Package DTA version 2.38.0 Index]