readApdRectangle: 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

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

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.

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]).

Author

Henrik Bengtsson

Examples

Run this code


# 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)
}