read.marrayLayout {marray}R Documentation

Create objects of class marrayLayout


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


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


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.



An object of class marrayLayout.



Jean Yang



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

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

### Setting control information.
swirl.gnames <- read.marrayInfo(file.path(datadir,""),, 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]