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)