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.

AuthorConor 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 publication2017-02-23 16:59:13
MaintainerConor Lawless <conor.lawless@ncl.ac.uk>
LicenseArtistic-2.0
Version0.0-44
http://qfa.r-forge.r-project.org/

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

Functions

bc2st Man page
bctimes Man page
benschopFromSource Man page
bsSamp Man page
buildBenschop Man page
buildComplexes Man page
buildGO Man page
buildPombeGO Man page
checkTarg Man page
colony.fit Man page
colony.info Man page
colonyzer.read Man page
complexesFromSource Man page
correlationReport Man page
data.fit Man page
de.fit Man page
drawSel Man page
dtl Man page
epiplot Man page
fastPwMahal Man page
findFit Man page
findImages Man page
findSimilar Man page
fitnessReport Man page
gen_logistic_maxslp Man page
getDeadLocations Man page
gethits Man page
getMissingGenotypes Man page
getMissingSGA Man page
getMode Man page
getNeighbours Man page
getResults Man page
getText Man page
globs Man page
Glogist Man page
growthcurve Man page
guess Man page
guessNEW Man page
index2pos Man page
iRVisDemo Man page
keybd Man page
lin.fit Man page
lm.epi Man page
loapproxfun Man page
logdraw Man page
logist Man page
makeBoundsQFA Man page
makeFitness Man page
makefits Man page
makePDF Man page
makePlot Man page
makeProfiles Man page
makeVisTool Man page
mdp Man page
mdr Man page
mdrmdp Man page
mkPlt Man page
mouse Man page
na2zero Man page
NAtoBlank Man page
normalisePlates Man page
nozero Man page
numericalfitness Man page
numerical_r Man page
orf2g Man page
orf2gdict Man page
orffit Man page
orfstat Man page
orfun Man page
perpRegression Man page
pgis Man page
pgis_bootstrap Man page
plateBoxplots Man page
plotAllReps Man page
plotFitsPoints Man page
plotGroupFits Man page
plotRepsDF Man page
plotRow Man page
plotSimilarFit Man page
posmake Man page
prepareTimecourse Man page
printSelected Man page
qfa.epi Man page
qfa.epiplot Man page
qfa.fit Man page
qfa.plot Man page
ratPlot Man page
rcget Man page
readMer Man page
readSGD Man page
report.epi Man page
reportExpts Man page
rod.read Man page
rod.write Man page
rowplot Man page
showDemo Man page
similarities Man page
slopeFun Man page
splitRegression Man page
sterr Man page
summarise Man page
summaryPlots Man page
sumsq Man page
targFun Man page
tconv Man page
testSlope Man page
timecourseImages Man page
toClipboard Man page
trep Man page
typemake Man page
varposget Man page

Files

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

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