read.marrayLayout {marray}R Documentation

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.

Details

Value

An object of class marrayLayout.

Note

Author(s)

Jean Yang yeehwa@stat.berkeley.edu

References

http://www.bioconductor.org/

Examples

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)

[Package marray version 1.8.0 Index]