Tools for Quantitative Fitness Analysis (QFA) of Arrayed Microbial Cultures Growing on Solid Agar Surfaces


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Documentation for package ‘qfa’ version 0.0-45

Help Pages

checkTarg checkTarg
colonyzer.read Reads raw cell density timecourse data from Colonyzer output files
correlationReport Correlation Report
data.fit Fitting generalised logistic model to growth data by least squares (using optim function)
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).
getMissingGenotypes getMissingGenotypes
getMissingSGA getMissingSGA
getNeighbours getNeighbours
Glogist Generalised Logistic growth curve model
growthcurve Wrapper function for generating QFA generalised logistic model fits to observed timecourse data
iRVisDemo Interactive fitness plots from Addinal et al. 2011 PLoS Genetics
loapproxfun Model free growth curve approximation
logist Logistic growth curve model
makeBoundsQFA Generate generalised logistic parameter bounds for QFA
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
numericalfitness Numerical fitness estimates from timecourse data
numerical_r Generates numerical fitnesses from experimental growth curve observations
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
readMer readMer
readSGD readSGD
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