marray (version 1.50.0)

read.marrayLayout: Create objects of class marrayLayout

Description

This function creates objects of class marrayLayout to store layout parameters for two-color cDNA microarrays.

Usage

read.marrayLayout(fname = NULL, ngr, ngc, nsr, nsc, pl.col = NULL, ctl.col = NULL, sub.col = NULL, notes = fname, skip, sep = "\t", quote = "\"", ...)

Arguments

fname
the name of the file that stores plate and control information. This is usually a file obtained from a database.
ngr
the number of rows of grids per image.
ngc
the number of columns of grids per image.
nsr
the number of rows of spots per grid.
nsc
the number of columns of spots per grid.
pl.col
the column number in fname that contains plate information.
ctl.col
the column number in fname that contains control information.
sub.col
the column number in fname that contains full ID information.
notes
object of class character, vector of explanatory text.
skip
the number of lines of the data file to skip before beginning to read data.
sep
the field separator character. Values on each line of the file are separated by this character. The default is to read a tab delimited file.
quote
the set of quoting characters. By default, this is disable by setting `quote="\""'.
...
further arguments to scan.

Value

An object of class marrayLayout.

References

http://www.bioconductor.org/

Examples

Run this code
datadir <- system.file("swirldata", package="marray")

### Reading in control information from file
skip <-  grep("Row", readLines(file.path(datadir,"fish.gal"), n=100)) - 1
swirl.layout <- read.marrayLayout(fname=file.path(datadir,"fish.gal"), ngr=4, ngc=4,
nsr=22, nsc=24, ctl.col=4, skip=skip)

### Setting control information.
swirl.gnames <- read.marrayInfo(file.path(datadir,"fish.gal"), info.id=4:5, labels=5, skip=21)
x <-  maInfo(swirl.gnames)[,1]
y <- rep(0, maNspots(swirl.layout))
y[x == "control"] <- 1
slot(swirl.layout, "maControls") <- as.factor(y)

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