readPlateData: Read Plate Data

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

Description

Parses platereader data files in CSV format, as exported by the plate reader software. Header IDs in the data file should match with IDs in the plate map, see readPlateMap. Pre-defined parsing functions exist for a couple of plate-readers. If your format is not implement, you can manually create simple data tables and use the function readSimplePlate

Usage

readPlateData(
  files,
  type,
  data.ids,
  interpolate = TRUE,
  time.range = c("common", "full"),
  time.conversion,
  verb = TRUE,
  ...
)

Arguments

files	list of one or more data files
type	pre-defined formats, as exported from platereaders; currently for BMG Optima and Mars v3.01 R2, ('BMG'), BMG Clariostar and Mars vXXX ('BMG2') and Biotek Synergy Mx ('Synergy'), BioLector ('BioLector'), BioLector Pro ('BioLectorPro'); TODO: define export protocols!
data.ids	an optional sub-selection of data types in the input file, as a list of strings
interpolate	if true a master time, the average time between distinct measurements of one timepoint, is calculated and all values are interpolated to this mastertime. This is currently obligatory for further processing. See function interpolatePlateTimes for details.
time.range	"common" requires that all data must have the same number of time-points, "full" interpolates the maximal available time range, using the mean time step of the mean of data-specific time vectors
time.conversion	conversion factor for the plate time, e.g., 1/3600 to convert from hours to seconds
verb	print messages if true
...	further parameters to plate-reader specific parsing functions

Value

a list of distinct measurement time-courses from one plate

Note

The original data is all interpolated to a common/average 'master' time

Author(s)

Rainer Machne [e-mail]

See Also

readSimplePlate, readBMGPlate, readSynergyPlate, readPlateMap, viewPlate

Examples

data.file <- system.file("extdata", "AP12.csv", package = "platexpress")
raw <- readPlateData(files=data.file, type="Synergy",
                     data.ids=c("600","YFP_50:500,535"),
                     dec=",", time.format="%H:%M:%S")

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