Tools for modelling the growth dynamics of arrays of large numbers of colonies and performing quantitative fitness analysis (QFA).


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Documentation for package ‘qfa’ version 0.0-10

Help Pages

colonyzer.read Reads raw cell density timecourse data from Colonyzer output files
correlationReport Correlation Report
dtl Culture Doubling Time for Generalised Logistic Function (as a function of time t)
fitnessReport Fitness Report
getDeadLocations Find dead cultures in SGA plates (1536 format), and report their location in spotted plates (384 format).
Glogist Generalised Logistic growth curve model
loapproxfun Model free growth curve approximation
logist Logistic growth curve model
makeFitness Generate QFA fitnesses
makeVisTool Making the visualisation tool
mdp Maximum Doubling Potential (MDP) for Generalised Logistic Function
mdr Maximum Doubling Rate (MDR) for Generalised Logistic Function
mdrmdp Fitness value for Generalised Logistic Function
normalisePlates Normalising culture fitness by plate
pgis Calculate strength and significance of genetic interaction.
plateBoxplots Plate Boxplots
qfa.epi Finds genetic interaction strengths and p-values
qfa.epiplot Makes an epistasis plot from the full results of qfa.epi
qfa.fit Growth curve modelling
qfa.plot Plots fitted model and data for all the colonies in results of qfa.fit
report.epi Normalising culture fitness by plate
rod.read Reading of ROD raw timecourse data. Deprecated.
rod.write Writes a synthetic ROD-like output file to hard-drive. Deprecated.
showDemo Show Demo
visToolDemo Interactive fitness plots from Addinal et al. 2011 PLoS Genetics