Man pages for bbakker1989/CINsim
Chromosomal Instability Simulator

animateHistoryAnimate karyotype history
appendCinsimAppend karyoSim results
calcClonalityCalculate frequency of clones in a population
calcConvergenceCalculate convergence towards the optimal karyotype...
calcDivProbCalculate probability of division
calcMissegCalculate adjusted probability of mis-segregation
calcQmodCalculate qMod to result in a desired value
calcSurProbCalculate probability of survival in a fitness-dependent...
calcSurProb2Calculate probability of survival in a fitness-dependent...
checkViabilityCheck viability based on karyotype
checkViabilityDavoliCheck viability based on karyotype
CinsimSimulate chromosomal instability.
Cinsim2Simulate chromosomal instability.
cnFreqCalculate copy number frequency
cnFreqListCalculate copy number frequency - summarizing a list of...
cnFreqTidyCalculate copy number frequency (tidy)
cnvHeatmapPlot a copy number heatmap.
cnvHeatmapListGenerate CNV heatmaps for all karyoSim objects in a list
compareChromosomesCompare chromosome measure across multiple simulations
compareSimsCompare multiple simulations
compileTidyDataCompile data from a list of parallel simulations
devFromModeCalculate the fraction of cells that deviate from the modal...
doMitosisPerform a round of mitosis with possible mis-segregations
getModeDetermine the mode in a vector of values.
getParametersGet sim parameters
makeCinsimListTidyCompile data from a list of parallel simulations (helper...
makeCinsimTidyTidy data summaries
makeKaryotypeReplicatesMake a list of karyotype matrices
makeKaryotypesMake a matrix of karyotypes
multiplotMultiple plot function
parallelCinsimRun multiple simulations in parallel
parallelCinSimRun multiple simulations in parallel
plotClonalitTidyPlot clonal frequencies (tidy)
plotClonalityPlot clonal frequencies
plotClonalityListPlot clonal frequencies (tidy)
plotDevFromModePlot the fraction of cells that deviate from the modal copy...
plotFirstMissegPlot degree of contribution to deviation from first...
plotKaryotypeMeasuresPlot karyotype measures per chromosome
plotKaryotypeMeasuresTidyTidy per chromosome karyotype measures
plotListTidyDataPlot summary data (based on a list of Cinsim objects)
plotMissegFreqPlot mis-segregation frequencies (tidy)
plotTidyDataPlot summary data (based on a one or several Cinsims)
qAneuploidyQuantify levels of aneuploidy
qHeterogeneityQuantify levels of heterogeneity
rtnormRestricted 'normal' distribution
runParallelSimsRun multiple simulations in parallel
simPlotsSimulation metrics plot
simPlotsTidyPlot summary data (based on a list of Cinsim objects)
startTimedMessageStart timed message
stopTimedMessageStop a timed message
bbakker1989/CINsim documentation built on Aug. 15, 2018, 4:37 a.m.