Reads a spatial subset of probe-level data from Affymetrix APD files

Description

Reads a spatial subset of probe-level data from Affymetrix APD files.

Usage

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## Default S3 method:
readApdRectangle(filename, xrange=c(0, Inf), yrange=c(0, Inf), ..., asMatrix=TRUE)

Arguments

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]).

Value

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.

Author(s)

Henrik Bengtsson

See Also

The readApd() method is used internally.

Examples

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# Local functions
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="[.](apd|APD)$")
files <- files[!file.info(files)$isdir]
if (length(files) > 0) {
  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)
}

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

Please suggest features or report bugs with the GitHub issue tracker.

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