readPlateMap: Read Plate Layout Map

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

Description

Parses a plate design file in CSV format. Rows and columns should be named as in the corresponding plate reader data files. TODO: causes empty groups in getGroups; because separate causes empty strings in first field instead of NA

Usage

readPlateMap(
  file,
  sep = "\t",
  fsep = "\n",
  fields,
  asep,
  afields,
  blank.id = "blank",
  nrows = 8,
  formatted = FALSE,
  header = TRUE
)

Arguments

file	text file containing the plate layout.
sep	column separator, as in read.table
fsep	within-field separator, separating the well-specific descriptors within well fields
fields	names for the field descriptors
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"
afields	field names which hold substance:amount pair information, see argument asep
blank.id	keyword that indicates blank wells. Blank wells can be combined with other well descriptors for separate blanking
nrows	number of rows to expect, defaults to 8 for rows A to H in a typical 96 well plate; TODO: get rid of this and instead check for rownames?
formatted	indicates whether the file is already in the required format; all other paramaters but 'sep' will be ignored
header	logical argument indicating the presence/absence of a header row in the layout file

Value

a table of well content descriptors, where the first column 'wells' maps the plate map to the data files.

Author(s)

Rainer Machne [e-mail]

See Also

readPlateData

Examples

plate.file <- system.file("extdata", "AP12_layout.csv", package = "platexpress")
plate <- readPlateMap(file=plate.file, blank.id="blank",fsep="\n", fields=c("strain","samples"))

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