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 numeric vector of cell (probe) indices specifying
which cells to updated. If NULL , all indices are considered. |
intensities |
A numeric vector of intensity values to be stored.
Alternatively, it can also be a named data.frame or matrix (or list )
where the named columns (elements) are the fields to be updated. |
stdvs |
A optional numeric vector . |
pixels |
A optional numeric vector . |
writeMap |
An optional write map. |
... |
Not used. |
verbose |
An integer specifying how much verbose details are
outputted. |
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 (http://www.braju.com/R/)
for (zzz in 0) { # Only so that 'break' can be used # Scan current directory for CEL files files <- list.files(pattern="[.](c|C)(e|E)(l|L)$") if (length(files) == 0) break # Create tempory copy of the CEL file filename <- file.path(tempdir(), sprintf("%s.tmp.cel", files[1])) if (file.exists(filename)) file.remove(filename) file.copy(from=files[1], to=filename) fields <- c("intensities", "stdvs", "pixels") # Cells to be updated idxs <- 1:2 # Get CEL header hdr <- readCelHeader(filename) # Get the original data cel <- readCel(filename, indices=idxs, readStdvs=TRUE, readPixels=TRUE) print(cel[fields]) cel0 <- cel # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # Square-root the intensities # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - updateCel(filename, indices=idxs, intensities=sqrt(cel$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) } # for (zzz in 0)