readPlateMap.old: Read Plate Layout Map

Description Usage Arguments Value Author(s) See Also Examples

View source: R/parsers.R

Description

Parses a plate design file in CSV format. Rows and columns should be named as in the corresponding plate reader data files.

Usage

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readPlateMap.old(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 [email protected]

See Also

readPlateData

Examples

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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 Nov. 9, 2018, 5:38 p.m.