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

Quantitative Fitness Analysis (QFA) is a complementary series of experimental and computational methods for estimating the fitness of thousands of microbial cultures in parallel. QFA is suitable for focussed, high-quality studies of the effect of genetic mutations or drug interventions on growth in model microbial organisms such as brewer's yeast. Culture growth is observed by time-lapse photography of solid agar plates inoculated with cultures in rectangular arrays. Growth curves are constructed by analysing image series using Colonyzer image analysis software (http://research.ncl.ac.uk/colonyzer) which converts images to arrays of cell density estimates. This R package is for a) fitting the generalised logistic model to potentially thousands of parallel growth curves, b) using inferred parameter values to calculate fitnesses for each culture and c) comparing fitnesses between QFA experiments with different genetic backgrounds or treatments to deduce interaction strengths. This package facilitates quantifying the fitness of thousands of independent microbial strains and tracking them throughout growth curve experiments. With appropriately designed experiments, qfa can also estimate genetic interaction strengths and produce epistasis plots.

Author
Conor Lawless <conor.lawless@ncl.ac.uk>, with contributions from Alexander Young <alextisyoung@gmail.com> and Darren Wilkinson <d.j.wilkinson@ncl.ac.uk>
Date of publication
2016-12-01 17:32:23
Maintainer
Conor Lawless <conor.lawless@ncl.ac.uk>
License
Artistic-2.0
Version
0.0-43
URLs

View on R-Forge

Man pages

checkTarg
checkTarg
colonyzer.read
Reads raw cell density timecourse data from Colonyzer output...
correlationReport
Correlation Report
datafit
Fitting generalised logistic model to growth data by least...
dtl
Culture Doubling Time for Generalised Logistic Function (as a...
fitnessReport
Fitness Report
getDeadLocations
Find dead cultures in SGA plates (1536 format), and report...
getMissingGenotypes
getMissingGenotypes
getMissingSGA
getMissingSGA
getNeighbours
getNeighbours
Glogist
Generalised Logistic growth curve model
growthcurve
Wrapper function for generating QFA generalised logistic...
iRVisDemo
Interactive fitness plots from Addinal et al. 2011 PLoS...
loapproxfun
Model free growth curve approximation
logist
Logistic growth curve model
makeBoundsQFA
Generate generalised logistic parameter bounds for QFA
makeFitness
Generate QFA fitnesses
mdp
Maximum Doubling Potential (MDP) for Generalised Logistic...
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...
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-Internal
Internal qfa Functions
qfa.plot
Plots fitted model and data for all the colonies in results...
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....
showDemo
Show Demo
visTool
Making the visualisation tool

Files in this package

qfa/DESCRIPTION
qfa/NAMESPACE
qfa/R
qfa/R/Exponential.R
qfa/R/Profiling.R
qfa/R/Visualisation.R
qfa/R/colonyRead.R
qfa/R/compareFitnesses.R
qfa/R/filteringGenes.R
qfa/R/qfa.R
qfa/R/reports.R
qfa/R/rodRead.R
qfa/R/stripSGA.R
qfa/R/visualiseCurves.R
qfa/build
qfa/build/vignette.rds
qfa/demo
qfa/demo/00Index
qfa/demo/fittingGrowthCurves.R
qfa/demo/telomereCap.R
qfa/inst
qfa/inst/doc
qfa/inst/doc/iRVis.Rmd
qfa/inst/doc/iRVis.html
qfa/inst/doc/qfa.Snw
qfa/inst/doc/qfa.pdf
qfa/inst/extdata
qfa/inst/extdata/DAL_QFA0139_Yku70_23_SDM_rhk_CTGN_vs_QFA0141_ura3_20_SDM_rhk_CTGN_MDRMDP_GIS.txt
qfa/inst/extdata/DAL_QFA0139_Yku70_30_SDM_rhk_CTGN_vs_QFA0141_ura3_27_SDM_rhk_CTGN_MDRMDP_GIS.txt
qfa/inst/extdata/DAL_QFA0139_Yku70_37_5_SDM_rhk_CTGN_vs_QFA0141_ura3_37_SDM_rhk_CTGN_MDRMDP_GIS.txt
qfa/inst/extdata/DAL_QFA0139_Yku70_37_SDM_rhk_CTGN_vs_QFA0141_ura3_37_SDM_rhk_CTGN_MDRMDP_GIS.txt
qfa/inst/extdata/DAL_QFA0140_cdc13-1_20_SDM_rhlk_CTGH_vs_QFA0141_ura3_20_SDM_rhk_CTGN_MDRMDP_GIS.txt
qfa/inst/extdata/DAL_QFA0140_cdc13-1_27_SDM_rhlk_CTGH_vs_QFA0141_ura3_27_SDM_rhk_CTGN_MDRMDP_GIS.txt
qfa/inst/extdata/DAL_QFA0140_cdc13-1_36_SDM_rhlk_CTGH_vs_QFA0141_ura3_37_SDM_rhk_CTGN_MDRMDP_GIS.txt
qfa/inst/extdata/DAL_QFA0141_ura3_27_SDM_rhk_CTGN_vs_QFA0141_ura3_20_SDM_rhk_CTGN_MDRMDP_GIS.txt
qfa/inst/extdata/DAL_QFA0141_ura3_37_SDM_rhk_CTGN_vs_QFA0141_ura3_20_SDM_rhk_CTGN_MDRMDP_GIS.txt
qfa/inst/extdata/FunctionalComplexes.txt
qfa/inst/extdata/GOAnnotation.txt
qfa/inst/extdata/GenerateDemoFiles.R
qfa/inst/extdata/LibraryDescription.txt
qfa/inst/extdata/ORF2GENE.txt
qfa/inst/extdata/SGD_features.tab
qfa/inst/extdata/URA3Control.dat
qfa/inst/extdata/URA3ExptDescription.txt
qfa/inst/extdata/cdc13-1ExptDescription.txt
qfa/inst/extdata/cdc13-1Query.dat
qfa/inst/extdata/pombeGOAnnotation.dat
qfa/inst/extdata/pombeGOAnnotation.txt
qfa/man
qfa/man/Glogist.Rd
qfa/man/checkTarg.Rd
qfa/man/colonyzer.read.Rd
qfa/man/correlationReport.Rd
qfa/man/datafit.Rd
qfa/man/dtl.Rd
qfa/man/fitnessReport.Rd
qfa/man/getDeadLocations.Rd
qfa/man/getMissingGenotypes.Rd
qfa/man/getMissingSGA.Rd
qfa/man/getNeighbours.Rd
qfa/man/growthcurve.Rd
qfa/man/iRVisDemo.Rd
qfa/man/loapproxfun.Rd
qfa/man/logist.Rd
qfa/man/makeBoundsQFA.Rd
qfa/man/makeFitness.Rd
qfa/man/mdp.Rd
qfa/man/mdr.Rd
qfa/man/mdrmdp.Rd
qfa/man/normalisePlates.Rd
qfa/man/numerical_r.Rd
qfa/man/numericalfitness.Rd
qfa/man/pgis.Rd
qfa/man/plateBoxplots.Rd
qfa/man/qfa-Internal.Rd
qfa/man/qfa.epi.Rd
qfa/man/qfa.epiplot.Rd
qfa/man/qfa.fit.Rd
qfa/man/qfa.plot.Rd
qfa/man/readMer.Rd
qfa/man/readSGD.Rd
qfa/man/report.epi.Rd
qfa/man/rod.read.Rd
qfa/man/rod.write.Rd
qfa/man/showDemo.Rd
qfa/man/visTool.Rd
qfa/vignettes
qfa/vignettes/QFAVisualisation0001.png
qfa/vignettes/QFAVisualisation0002.png
qfa/vignettes/QFAVisualisation0003.png
qfa/vignettes/RatioPlot0001.png
qfa/vignettes/RatioPlot0002.png
qfa/vignettes/RatioPlot0002a.png
qfa/vignettes/RatioPlot0003.png
qfa/vignettes/RatioPlot0004.png
qfa/vignettes/RatioPlot0005.png
qfa/vignettes/RatioPlot0006.png
qfa/vignettes/RatioPlot0007.png
qfa/vignettes/RatioPlot0008.png
qfa/vignettes/iRVis.Rmd
qfa/vignettes/qfa.Snw