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 |
ctl.col |
the column number in |
sub.col |
the column number in |
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 |
An object of class marrayLayout.
Jean Yang yeehwa@stat.berkeley.edu
http://www.bioconductor.org/
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)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.