divisionMPGenerationDpd: Simulate an astrocyte lineage

In marionbetizeau/CerebellumAstrocyteSimulation: Simulate Astrocyte Lineages

Description

Simulate an astrocyte lineage

Usage

divisionMPGenerationDpd(motherCell = currentCell, cloneOutput = cloneTable,
  transitionMatrix = list(transition.Progenitor, transition.Astro,
  firstPostMitoticCell), maxCount = 1e+05, parameterInterpolation = T)

Arguments

motherCell	the information table of the mother cell
cloneOutput	the initialized clone table with the 1st cell information
transitionMatrix	a list specifying the transition matrix of the particular progenitor type: - transition.Progenitor : list of 3 elements defining the probabilities of cell cycle exit vs amplification of the progenitor, as well as the potential types produced probability Matrix with columns: probabilities of generating a MP (1st column), or an Astrocyte (2nd column), rows : for each generation in the simulated lineage (number of rows can vary) type The corresponding names of different possible outcome, in the same order as the columns of the probability matrix (MP, Astro) (number of types correponds to the number of columns of the above probability matrix) generationInterval Vector of length corresponding to the number of generations, length equal to the number of rows of the matrix probability - transition.Astro : probabilities of generating the different astrocyte types after cell cycle exit probability Matrix with columns: probabilities of generating a BG (1st column), a GLA (2nd column), or a WMA (3rd column) rows : for each generation in the simulated lineage (number of rows can vary) type The corresponding names of different possible outcome, in the same order as the columns of the probability matrix (BG, GLA, WMA) (number of types correponds to the number of columns of the above probability matrix) generationInterval Vector of length corresponding to the number of generations, length equal to the number of rows of the matrix probability - firstPostMitoticCell : for the one-cell clones, proportions of the observed astrocyte types
maxCount	number of trials after which the function will stop and return an error message if the lineage never stops (stochasticity issue, the lineage stops when all cells differentiate. If the probability of cell cycle exit is too low, some cell might keep on proliferating indefinitely.)
parameterInterpolation	boolean indicating whether interpolation was performed on the input data (always TRUE in the published simulations)

Value

cloneTable: dataframe containing the information about the simulated lineage

motherID

ID of the mother of the current cell

cellID

ID of the current cell

type

Type of the current cell

timepoint

Generation the current cell is born. Mother cell is initialized at generation 1

See Also

currentCell cloneTable transition.MP transition.Astro firstPostMitoticCell

Examples

# Simulation of a lineage with a multipotent progenitor as initial cell.
cloneTable  <- divisionMPGenerationDpd(motherCell = currentCell, 
                                       cloneOutput = cloneTable, 
                                       transitionMatrix = list(transition.MP, transition.Astro, firstPostMitoticCell),
                                       maxCount = 100000)

marionbetizeau/CerebellumAstrocyteSimulation documentation built on May 14, 2019, 7:20 p.m.