readCelRectangle {affxparser} | R Documentation |
Reads a spatial subset of probe-level data from Affymetrix CEL files.
readCelRectangle(filename, xrange=c(0, Inf), yrange=c(0, Inf), ..., asMatrix=TRUE)
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]). |
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.
Henrik Bengtsson (http://www.braju.com/R/)
The readCel
() method is used internally.
############################################################## 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 # ##############################################################