analyzeGrowthCurves: Calculate doubling times for liquid culutres in multiwell...
In whitwort/growthCurves: Microbial growth curve analysis

Description Usage Arguments Value

View source: R/growthCurves.R

This function loads one or more tables, a set of well label annotations (if given), and then calculates doubling times (doublingTime) and produces individual and composite OD plots (makeODPlots). The default analysis pipeline can be tuned by passing any arguments accepted by table parsers, annotation parsers, data filters, analysis functions and visualization functions.

analyzeGrowthCurves(tablePath, savePath = NULL, tableParser = magellanTable,
  annotationPath = NULL, annotationParser = plateSetup,
  plateLabels = default.plate.96, filters = c(default.lagFilter,
  default.plateauFilter), zipPath = NULL, ...)

`tablePath`	path on the local file system to be passed to the tableParser
`savePath`	optional path to a directory where results should be saved; defaults to NULL which means that no tables or images will be saved.
`tableParser`	a function to use to parse tables; see `csvTable` for an example.
`annotationPath`	path on the local file system to pass to the annotationParser
`annotationParser`	a function to use to parse annotation files; see `plateSetup` for an example.
`plateLabels`	a matrix of well labels that matches the shape of the plate data being analyzed. Two default layouts are provided: `default.plate.96` and `default.plate.384`
`filters`	a list of unnamed functions which will be used to filter OD data; see `default.lagFilter` and `default.plateauFilter` for examples.
`zipPath`	path on the local file system where a new zipfile archive should be written containing all files produced in the analysis. Defaults to NULL which indicates no zip file should be created.
`...`	all additional arguments are passed along to the parser, filter, analysis and visualization functions that recieve them.