readCelUnits {affxparser} | R Documentation

## Reads probe-level data ordered as units (probesets) from one or several Affymetrix CEL files

### Description

Reads probe-level data ordered as units (probesets) from one or several Affymetrix CEL files by using the unit and group definitions in the corresponding Affymetrix CDF file.

### Usage

    readCelUnits(filenames, units=NULL, stratifyBy=c("nothing", "pmmm", "pm", "mm"), cdf=NULL, ..., addDimnames=FALSE, dropArrayDim=TRUE, transforms=NULL, reorder=TRUE, readMap=NULL, verbose=FALSE)

### Arguments

`filenames` | The filenames of the CEL files.
`units` | An `integer` `vector` of unit indices specifying which units to be read. If `NULL`, all units are read.
`stratifyBy` | Argument passed to low-level method `readCdfUnits`.
`cdf` | A `character` filename of a CDF file, or a CDF `list` structure. If `NULL`, the CDF file is searched for by `findCdf`() first starting from the current directory and then from the directory where the first CEL file is.
`...` | Arguments passed to low-level method `readCel`, e.g. `readXY` and `readStdvs`.
`addDimnames` | If `TRUE`, dimension names are added to arrays, otherwise not. The size of the returned CEL structure in bytes increases by 30-40% with dimension names.
`dropArrayDim` | If `TRUE` and only one array is read, the elements of the group field do not have an array dimension.
`transforms` | A `list` of exactly `length(filenames)` `function`s. If `NULL`, no transformation is performed. Intensities read are passed through the corresponding transform function before being returned.
`reorder` | If `TRUE`, cell indices are read in order to speed up the reading. If `FALSE`, cells are read in the order as given. For more details, see help on the same argument in `readCel`().
`readMap` | A `vector` remapping cell indices to file indices. If `NULL`, no mapping is used.
`verbose` | Either a `logical`, a `numeric`, or a `Verbose` object specifying how much verbose/debug information is written to standard output. If a Verbose object, how detailed the information is is specified by the threshold level of the object. If a numeric, the value is used to set the threshold of a new Verbose object. If `TRUE`, the threshold is set to -1 (minimal). If `FALSE`, no output is written (and neither is the R.utils package required).

### Value

A named `list` with one element for each unit read. The names corresponds to the names of the units read. Each unit element is in turn a `list` structure with groups (aka blocks). Each group contains requested fields, e.g. `intensities`, `stdvs`, and `pixels`. If more than one CEL file is read, an extra dimension is added to each of the fields corresponding, which can be used to subset by CEL file.
Note that neither CEL headers nor information about outliers and masked cells are returned. To access these, use `readCelHeader`() and `readCel`().

### Author(s)

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

### References

[1] Affymetrix Inc, Affymetrix GCOS 1.x compatible file formats, June 14, 2005. http://www.affymetrix.com/support/developer/

### See Also

Internally, `readCelHeader`(), `readCdfUnits`() and `readCel`() are used.

### Examples

    ##############################################################
    if (require("AffymetrixDataTestFiles")) {            # START #
    ##############################################################

    # Search for some available CEL files
    path <- system.file("rawData", package="AffymetrixDataTestFiles")
    files <- findFiles(pattern="[.](cel|CEL)$", path=path, recursive=TRUE, firstOnly=FALSE)
    files <- grep("FusionSDK_Test3", files, value=TRUE)
    files <- grep("Calvin", files, value=TRUE)

    # Fake more CEL files if not enough
    files <- rep(files, length.out=5)

    print(files);

    # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    # Benchmarking reading cells in order or not.
    #
    # The difference will be large the more files that are read.
    # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
    units <- 56:256
    nunits <- length(units);

    nfiles <- length(files);

    t1 <- system.time({
      cel <- readCelUnits(files, units=units, reorder=TRUE)
    })[3]
    cat(sprintf("Time   [ordered]: %6.2fs = %.2fms/(unit & array) [1.00x]\n",
                                              t1, 1000*t1/nunits/nfiles))
    rm(cel); gc()

    t2 <- system.time({
      cel <- readCelUnits(files, units=units, reorder=FALSE)
    })[3]
    cat(sprintf("Time [unordered]: %6.2fs = %.2fms/(unit & array) [%.2fx]\n",
                                       t2, 1000*t2/nunits/nfiles, t2/t1))
    rm(cel); gc()

    # Clean up
    rm(files, t1, t2)

    ##############################################################
    }                                                     # STOP #
    ##############################################################

[Package affxparser version 1.10.2 Index]