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

Description Usage Arguments Value Author(s) See Also Examples

View source: R/readCelRectangle.R

Description

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

Usage

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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

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

affxparser documentation built on Nov. 1, 2018, 2:25 a.m.