| readApdRectangle {aroma.apd} | R Documentation |
Reads a spatial subset of probe-level data from Affymetrix APD files.
## Default S3 method: readApdRectangle(filename, xrange=c(0, Inf), yrange=c(0, Inf), ..., asMatrix=TRUE)
filename |
The pathname of the APD file. |
xrange |
A numeric vector of length two giving the left
and right coordinates of the cells to be returned. |
yrange |
A numeric vector of length two giving the top
and bottom coordinates of the cells to be returned. |
... |
Additional arguments passed to readApd(). |
asMatrix |
If TRUE, the APD data fields are returned as
matrices with element (1,1) corresponding to cell
(xrange[1],yrange[1]). |
A named list APD structure similar to what readApd().
In addition, if asMatrix is TRUE, the APD data fields
are returned as matrices, otherwise not.
Henrik Bengtsson (http://www.braju.com/R/)
The readApd() method is used internally.
for (zzz in 0) {
rotate270 <- function(x, ...) {
x <- t(x)
nc <- ncol(x)
if (nc < 2) return(x)
x[,nc:1,drop=FALSE]
}
# Scan current directory for APD files
files <- list.files(pattern="[.](a|A)(p|P)(d|D)$")
files <- files[!file.info(files)$isdir]
if (length(files) == 0)
break
apdFile <- files[1];
# Read APD intensities in the upper left corner
apd <- readApdRectangle(apdFile, xrange=c(0,250), yrange=c(0,250))
z <- rotate270(apd$intensities)
sub <- paste("Chip type:", apd$header$chipType)
image(z, col=gray.colors(256), axes=FALSE, main=apdFile, sub=sub)
text(x=0, y=1, labels="(0,0)", adj=c(0,-0.7), cex=0.8, xpd=TRUE)
text(x=1, y=0, labels="(250,250)", adj=c(1,1.2), cex=0.8, xpd=TRUE)
# Clean up
rm(rotate270, files, apdFile, apd, z, sub)
} # for (zzz in 0)
rm(zzz)