DTA.dynamic.estimate uses an experiment, given by a phenotype matrix, data matrix and the number of uridines for each gene to estimate synthesis and decay rate of the genes.

1 | ```
DTA.dynamic.estimate(phenomat = NULL,datamat = NULL,tnumber = NULL,ccl = NULL,mRNAs = NULL,reliable = NULL,mediancenter = TRUE,usefractions = "LandT",LtoTratio = NULL,ratiomethod = "tls",largest = 5,weighted = TRUE,relevant = NULL,check = TRUE,error = TRUE,samplesize = 1000,confidence.range = c(0.025,0.975),bicor = TRUE,condition = "",upper = 700,lower = 500,save.plots = FALSE,resolution = 1,folder = NULL,fileformat = "jpeg",totaloverwt = 1,sr.vs.dr.folds.lims = c(-5,5),te.vs.to.folds.lims = c(-6,6),robust = FALSE,clusters = "sr",ranktime = NULL,upperquant = 0.8,lowerquant = 0.6,notinR = FALSE,RStudio = FALSE,simulation = FALSE,sim.object = NULL)
``` |

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

`datamat` |
A matrix, containing the measurements from U, L and T, according to the design given in phenomat. Matrix should only contain the rows of phenomat as columns. |

`tnumber` |
Integer vector, containing the numbers of uridines. Elements should have the rownames of datamat. |

`ccl` |
The cell cycle length of the cells. |

`mRNAs` |
Estimated number of mRNAs in a cell (optional). |

`reliable` |
Vector of 'reliable' genes, which are used for parameter estimation. |

`mediancenter` |
Should the quotient Labeled/Total resp. Unlabeled/Total be rescaled to a common median over it's replicates before building the genewise median. |

`usefractions` |
From which fractions should the decay rate be calculated: "LandT", "UandT" or "both". |

`LtoTratio` |
Coefficient to rescale Labeled/Total. Is estimated from the data, if not specified. See ratiomethod. |

`ratiomethod` |
Choose the regression method to be used, possible methods are: "tls", "bias" and "lm". For details, see supplemental material of Sun et al. (see references). |

`largest` |
Percentage of largest residues from the first regression not to be used in the second regression step. For details, see supplemental material of Sun et al. (see references). |

`weighted` |
Should the regression be weighted with 1/(Total^2 + median(Total))? |

`relevant` |
Choose the arrays to be used for halflives calculation, vector due to nr (=replicate number) in phenomat. |

`check` |
If check = TRUE, control messages and plots will be generated. |

`error` |
If TRUE, the measurement error is assessed by means of an error model and resampling to gain confidence regions. |

`samplesize` |
Error model samplesize for resampling. |

`confidence.range` |
Confidence region for error model as quantiles. Interval should be between 0 and 1. |

`bicor` |
Should the labeling bias be corrected? |

`condition` |
String, to be added to the plotnames. |

`upper` |
Upper bound for labeling bias estimation. For details, see supplemental material of Sun et al. (see references). |

`lower` |
Lower bound for labeling bias estimation. For details, see supplemental material of Sun et al. (see references). |

`save.plots` |
If save.plots = TRUE, control plots will be saved. |

`resolution` |
Resolution scaling factor for plotting. |

`folder` |
Path to the folder, where to save the plots. |

`fileformat` |
Fileformat for plots to be saved. See |

`totaloverwt` |
Will be available in the very near future for comparative DTA data. |

`sr.vs.dr.folds.lims` |
Limits of the folds plot (dr vs sr). |

`te.vs.to.folds.lims` |
Limits of the folds plot (LT vs LE). |

`robust` |
If robust = TRUE, LE resp. LT is chosen instead of sr resp. dr. |

`clusters` |
should the dr vs sr folds be plotted with clusters, choose 'sr', 'dr' for cluster selection or 'none' to omit it |

`ranktime` |
at which time should the rankgain be calculated, default is the last column |

`upperquant` |
upper quantile for cluster selection |

`lowerquant` |
lower quantile for cluster selection |

`notinR` |
Should plots be not plotted in R. |

`RStudio` |
For RStudio users. Suppresses the opening of a new device, as RStudio allows only one. |

`simulation` |
True, if data was generated by |

`sim.object` |
Simulation object created by |

`DTA.dynamic.estimate`

returns a list, where each entry contains the estimation results for all replicates of one timecourse timepoint. Each result contains the following entries

`triples` |
Mapping of each fraction and experiment to its corresponding column in the data matrix. |

`plabel` |
The labeling efficiency. For details, see the vignette. |

`LtoTratio` |
Estimated ratio of labeled to total fraction. |

`UtoTratio` |
Estimated ratio of unlabeled to total fraction. |

`LtoUratio` |
Estimated ratio of labeled to unlabeled fraction. |

`correcteddatamat` |
Labeling bias corrected data matrix. |

`drmat` |
Decay rates for each replicate. The last column gives the median decay rates. |

`dr` |
Median decay rates. The last column of drmat. |

`dr.confidence` |
Confidence regions of decay rates. |

`hlmat` |
Half-lives for each replicate. The last column gives the median half-lifes. |

`hl` |
Median half-lives. The last column of hlmat. |

`hl.confidence` |
Confidence regions of half-lives. |

`TEmat` |
Total expression for each replicate. The last column gives the median total expression values. |

`TE` |
Median total expression values. The last column of TEmat. |

`TE.confidence` |
Confidence regions of total expression values. |

`LEmat` |
Labeled expression for each replicate. The last column gives the median labeled expression values. |

`LE` |
Median labeled expression values. The last column of LEmat. |

`LE.confidence` |
Confidence regions of labeled expression values. |

`UEmat` |
Unlabeled expression for each replicate. The last column gives the median unlabeled expression values. (Only if unlabeled values exist in the experiment) |

`UE` |
Median unlabeled expression values. The last column of UEmat. (Only if unlabeled values exist in the experiment) |

`UE.confidence` |
Confidence regions of unlabeled expression values. |

`srmat` |
Synthesis rates for each replicate. The last column gives the median synthesis rates. |

`sr` |
Median synthesis rates. The last column of srmat. |

`sr.confidence` |
Confidence regions of synthesis rates. |

`LtoTmat` |
Labeled to total ratio for each replicate. The last column gives the median labeled to total ratios. |

`LtoT` |
Median labeled to total ratios. The last column of LtoTmat. |

`LtoT.confidence` |
Confidence regions of labeled to total ratios. |

`UtoTmat` |
Unlabeled to total ratio for each replicate. The last column gives the median unlabeled to total ratios. |

`UtoT` |
Median unlabeled to total ratios. The last column of UtoTmat. |

`UtoT.confidence` |
Confidence regions of unlabeled to total ratios. |

`Rsrmat` |
Rescaled synthesis rates for each replicate, if parameter |

`Rsr` |
Rescaled median synthesis rates. The last column of Rsrmat. |

`globaldrmat` |
Decay rate for each replicate. Reciprocally weighted by the total expression. Last element contains (weighted) median decay rate. |

`globaldr` |
(Weighted) median decay rate. |

Bjoern Schwalb schwalb@lmb.uni-muenchen.de

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 6 | ```
dataPath = system.file("data", package="DTA")
load(file.path(dataPath, "Miller2011dynamic.RData"))
### for control plots set 'check = TRUE' ###
res = DTA.dynamic.estimate(Sc.phenomat.dynamic,Sc.datamat.dynamic,Sc.tnumber,ccl = 150,mRNAs = 60000,reliable = Sc.reliable.dynamic,LtoTratio = rep(0.1,7),check = FALSE)
``` |

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