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

In HenrikBengtsson/affxparser: Affymetrix File Parsing SDK

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

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 #
##############################################################

HenrikBengtsson/affxparser documentation built on Feb. 9, 2024, 3:13 a.m.