updateCel {affxparser} | R Documentation |
Updates a CEL file.
updateCel(filename, indices=NULL, intensities=NULL, stdvs=NULL, pixels=NULL, writeMap=NULL, ..., verbose=0)
filename |
The filename of the CEL file. |
indices |
A |
intensities |
A |
stdvs |
|
pixels |
|
writeMap |
An optional write map. |
... |
Not used. |
verbose |
An |
Currently only binary (v4) CEL files are supported. The current version of the method does not make use of the Fusion SDK, but its own code to navigate and update the CEL file.
Returns (invisibly) the pathname of the file updated.
Henrik Bengtsson
############################################################## if (require("AffymetrixDataTestFiles")) { # START # ############################################################## # Search for some available Calvin CEL files path <- system.file("rawData", package="AffymetrixDataTestFiles") files <- findFiles(pattern="[.](cel|CEL)$", path=path, recursive=TRUE, firstOnly=FALSE) files <- grep("FusionSDK_HG-U133A", files, value=TRUE) files <- grep("Calvin", files, value=TRUE) file <- files[1] # Convert to an XDA CEL file filename <- file.path(tempdir(), basename(file)) if (file.exists(filename)) file.remove(filename) convertCel(file, filename) fields <- c("intensities", "stdvs", "pixels") # Cells to be updated idxs <- 1:2 # Get CEL header hdr <- readCelHeader(filename) # Get the original data cel <- readCel(filename, indices=idxs, readStdvs=TRUE, readPixels=TRUE) print(cel[fields]) cel0 <- cel # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # Square-root the intensities # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - updateCel(filename, indices=idxs, intensities=sqrt(cel$intensities)) cel <- readCel(filename, indices=idxs, readStdvs=TRUE, readPixels=TRUE) print(cel[fields]) # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # Update a few cell values by a data frame # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - data <- data.frame( intensities=cel0$intensities, stdvs=c(201.1, 3086.1)+0.5, pixels=c(9,9+1) ) updateCel(filename, indices=idxs, data) # Assert correctness of update cel <- readCel(filename, indices=idxs, readStdvs=TRUE, readPixels=TRUE) print(cel[fields]) for (ff in fields) { stopifnot(all.equal(cel[[ff]], data[[ff]], .Machine$double.eps^0.25)) } # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # Update a region of the CEL file # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # Load pre-defined data side <- 306 pathname <- system.file("extras/easternEgg.gz", package="affxparser") con <- gzfile(pathname, open="rb") z <- readBin(con=con, what="integer", size=1, signed=FALSE, n=side^2) close(con) z <- matrix(z, nrow=side) side <- min(hdr$cols - 2*22, side) z <- as.double(z[1:side,1:side]) x <- matrix(22+0:(side-1), nrow=side, ncol=side, byrow=TRUE) idxs <- as.vector((1 + x) + hdr$cols*t(x)) # Load current data in the same region z0 <- readCel(filename, indices=idxs)$intensities # Mix the two data sets z <- (0.3*z^2 + 0.7*z0) # Update the CEL file updateCel(filename, indices=idxs, intensities=z) # Make some spatial changes rotate270 <- function(x, ...) { x <- t(x) nc <- ncol(x) if (nc < 2) return(x) x[,nc:1,drop=FALSE] } # Display a spatial image of the updated CEL file cel <- readCelRectangle(filename, xrange=c(0,350), yrange=c(0,350)) z <- rotate270(cel$intensities) sub <- paste("Chip type:", cel$header$chiptype) image(z, col=gray.colors(256), axes=FALSE, main=basename(filename), 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="(350,350)", adj=c(1,1.2), cex=0.8, xpd=TRUE) # Clean up file.remove(filename) rm(files, cel, cel0, idxs, data, ff, fields, rotate270) ############################################################## } # STOP # ##############################################################