R: Reads a spatial subset of probe-level data from Affymetrix...

readApdRectangle {aroma.apd} | R Documentation

## 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

    ## 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

    # 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)
    }

[Package aroma.apd version 0.6.0 Index]