grofit_plate: high-level wrapper for 'grofit'

In raim/platexpress: Inspection and Analysis of Microbial Growth and Gene Expression Data

Description

Calls grofit directly from platexpress plate data and layout, using established settings. Please see the documentation of package grofit for details of the fitting procedure. This high-level wrapper uses platexpress functions data2grofit, grofit.2.control, gcFit.2 to convert data, to set parameters and to call grofit.

Usage

grofit_plate(
  data,
  plate,
  yid,
  amount,
  fields = c("strain", "medium", "substance"),
  control,
  model.type = c("richards", "logistic", "gompertz.exp", "gompertz"),
  nboot.gc = 100,
  plot = TRUE,
  interactive = FALSE,
  verb = TRUE,
  col = "#0000FF",
  ...
)

Arguments

data	a platexpress data set, see readPlateData
plate	plate layout map, see readPlateMap, columns of this map can be converted to grofit data annotation, and results will be returned in the same order of wells
yid	data ID of the data to be converted; default is to take the first of data$dataIDs
amount	name of a column in plate that provides a numeric 'amount', to be used as a 'dose' annotation in grofit
fields	column IDs in the plate layout map to be used for grofit data annotation; if plate is not missing at least 1 column is required
control	an object of class grofit.control with an additional parameter plot, as provided by the platexpress function grofit.2.control; if present arguments model.type, nboot.gc and plot will be ignored (unless the latter is not present)
model.type	models that grofit will attempt to fit, see grofit.control; will be igonred if control is passed directly
nboot.gc	numbers of bootstrap samples, see grofit.control; will be igonred if control is passed directly
plot	set to TRUE for plots even without interactive use
interactive	set to TRUE for interactive growth curve fitting
verb	print messages
col	color of the model data in the plate data object
...	further arguments to grofit.2.control

Details

The function returns a list of fits, as returnted by platexpress's gcFit.2, a copy of grofit's gcFit with modified plotting and interactive behaviour but otherwise identical. All run parameters of gcFit can be set via option control, where platexpress' grofit.2.control add the differing plot and interactive settings.

raim/platexpress documentation built on Jan. 18, 2022, 1:41 p.m.