updateCel {affxparser} | R Documentation

## Updates a CEL file

### Description

Updates a CEL file.

### Usage

    updateCel(filename, indices=NULL, intensities=NULL, stdvs=NULL, pixels=NULL, writeMap=NULL, ..., verbose=0)

### Arguments

`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.

### Details

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.

### Value

Returns (invisibly) the pathname of the file updated.

### Author(s)

Henrik Bengtsson (http://www.braju.com/R/)

### Examples

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

[Package affxparser version 1.16.0 Index]