Man pages for carinademel/RNAlife
Quantifying kinetic parameters to determine the RNA life cycle
| dta.model | DTA model function for labeled RNA |
| dta.model.decay | Exponential decay of unlabeled RNA |
| dta.model.labeled | DTA model function for labeled RNA |
| dta.plot | Function to create a plot based on synthesis and degradation... |
| dta.plot.decay | Function to plot the decay of the unlabeled RNA (remaining... |
| dta.plot.labeled | Function to create a plot based on a DTA model result |
| estimateGeneDispersion | Estimates gene-specific dispersion estimates for total and... |
| estimate.rates | Wrapper function to estimate gene- and time specific... |
| fitAlphaBeta.log.reparam | Estimate best alpha = labeled amount and best beta =... |
| gene.counts | Count matrix for genes |
| getExpectedCounts | Implementation of Equation 1 and 2 -> get alpha and beta |
| initial.guess | Function to estimate initial alpha and beta values based on... |
| initial.guess.alpha | Calculate initial alpha values (labeled RNA) by closed form... |
| initial.guess.beta | Calculate initial beta values (unlabeled RNA amount) by... |
| samples | Data frame explaining the experimental samples |
| spikein.counts | Count matrix for artificial spike-ins |
| spikein.dataframe | Function to create a data frame to be used for the GLM |
| spikein.labeling | Labeling vector for artificial spike-ins |
| spikein.lengths | Length vector for artificial spike-ins |
| spikein.normalization | function to estimate normalization parameters based on... |
