readCelRectangle {affxparser} | R Documentation

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

### Description

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

### Usage

    readCelRectangle(filename, xrange=c(0, Inf), yrange=c(0, Inf), ..., asMatrix=TRUE)

### Arguments

`filename` | The pathname of the CEL 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 `readCel`().
`asMatrix` | If `TRUE`, the CEL data fields are returned as matrices with element (1,1) corresponding to cell (xrange[1],yrange[1]).

### Value

A named `list` CEL structure similar to what `readCel`(). In addition, if `asMatrix` is `TRUE`, the CEL data fields are returned as matrices, otherwise not.

### Author(s)

Henrik Bengtsson (http://www.braju.com/R/)

### See Also

The `readCel`() method is used internally.

### Examples

    ##############################################################
    if (require("AffymetrixDataTestFiles")) {            # START #
    ##############################################################

    rotate270 <- function(x, ...) {
      x <- t(x)
      nc <- ncol(x)
      if (nc < 2) return(x)
      x[,nc:1,drop=FALSE]
    }

    # Search for some available CEL files
    path <- system.file("rawData", package="AffymetrixDataTestFiles")
    file <- findFiles(pattern="[.](cel|CEL)$", path=path, recursive=TRUE)

    # Read CEL intensities in the upper left corner
    cel <- readCelRectangle(file, xrange=c(0,250), yrange=c(0,250))
    z <- rotate270(cel$intensities)
    sub <- paste("Chip type:", cel$header$chiptype)
    image(z, col=gray.colors(256), axes=FALSE, main=basename(file), 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, file, cel, z, sub)

    ##############################################################
    }                                                     # STOP #
    ##############################################################

[Package affxparser version 1.16.0 Index]