readExperiment: High-level interface of 'platexpress'

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

Description

This high-level wrapper allows to load a platereader experiment and its layout file, do blank corrections, and replicate groupings.

Usage

readExperiment(
  files,
  type,
  dsep,
  time.range = c("full"),
  time.conversion = 1/3600,
  layout,
  sep = ";",
  fsep = ";",
  asep = ":",
  blank.id = "blank",
  fields,
  afields,
  skip.wells,
  blank = FALSE,
  blank.data,
  base = 0,
  group1,
  group2,
  group2.color,
  ...
)

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!
dsep	sep parameter for data file, see readPlateData
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
layout	the text file containing the plate layout information, see argument file in readPlateMap
sep	column separator, as in read.table
fsep	within-field separator, separating the well-specific descriptors within well fields
asep	a separator for substance:amount pairs, eg. to indicate amount of an inducer or a nutrient, can only be used together with argument afields, eg. use asep=":", afields="inducer"
blank.id	keyword that indicates blank wells. Blank wells can be combined with other well descriptors for separate blanking
fields	names for the field descriptors
afields	field names which hold substance:amount pair information, see argument asep
skip.wells	skip these wells from all analyses, see argument skip in skipWells
blank	call correctBlanks to blank data
blank.data	subset of data to blank, see argument yids in function correctBlanks
base	optional minimal value; all values will be raised by the same amount using the function adjustBase via function correctBlanks
group1	plate layout column to be used for coarse grouping, via function getGroups, eg. "strains"
group2	plate layout column to be used for fine grouping, via function getGroups, eg. "inducer amount")
group2.color	numeric plate layout column to be used for group2 coloring, via function groupColors, eg. "amount"
...	further parameters to plate-reader specific parsing functions

Details

Calls, in this order the platexpress functions readPlateData, readPlateMap; optionally: skipWells, and correctBlanks, and getGroups. Please see the help files of these functions for details on parameters.

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