qfa.testdata: A screen of three Staphylococcus aureus strains arranged in a...
In JulBaer/baQFA: Quantitative Fitness Analysis Version 2

qfa.testdata

R Documentation

A screen of three Staphylococcus aureus strains arranged in a grid

Description

This is the result of a call of Colonyzer.read of an experiment in which three different Staphylococcus aureus strains have been grown in a grid. The three strains are Cowan and JE2 lab strains and a clinical isolate named CI1149.

Usage

data(qfa.testdata)

Format

data.frame

References

unpublished

Examples

data(qfa.testdata)
#Strip non-experimental edge cultures
qfa.testdata=qfa.testdata[(qfa.testdata$Row!=1) & (qfa.testdata$Col!=1) & (qfa.testdata$Row!=8) & (qfa.testdata$Col!=12),]
# Define which measure of cell density to use
qfa.testdata$Growth = qfa.testdata$Intensity
GmpFit = qfa.fit2(qfa.testdata, inocguess=NULL, detectThresh=0, globalOpt=F, AUCLim=NA, TimeFormat="h", Model="Gmp")
# Construct fitness measures
GmpFit = makeFitness2(GmpFit, AUCLim=NA, plotFitness="All", filename="Example_Gmp_fitness.pdf")
# Create plot
qfa.plot2("Example_Gmp_GrowthCurves.pdf", GmpFit, qfa.testdata, maxt=30)

JulBaer/baQFA documentation built on Feb. 19, 2023, 10:32 p.m.