numericalfitness: Numerical fitness estimates from timecourse data

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

Description

Generates numerical area under curve (nAUC) and numerical single time point (nSTP) measures of fitness. This function generates a piecewise linear interpolation between the available datapoints in the data frame obsdat. Interpolation is continued beyond the observed range of times assuming a density equal to the nearest observed time.

nAUC is the area under the interpolating function, and is estimated by integrating between limits 0 and AUCLim. nSTP is the interpolated cell density estimate at t=STP.

Usage

numericalfitness(obsdat,AUCLim,STP,nrate=FALSE)

Arguments

obsdat	A data frame containing a numeric Expt.Time column (time since culture inoculation, typically in days) and a numeric Growth column (typically cell density estimates estimated from a timeseries of culture photographs, quantified by software such as Colonyzer: http://research.ncl.ac.uk/colonyzer/)
AUCLim	Upper limit of integration for calculating area under growth curve as a measure of culture fitness
STP	Single time point at which to estimate cell density (measure of fitness, as used in SGA for example: http://en.wikipedia.org/wiki/Synthetic_genetic_array)
nrate	Calculate numerical growth rate phenotypes and add these to the output results.

Value

A named vector specifying nAUC and nSTP.

qfa documentation built on Feb. 22, 2020, 3:01 a.m.