import.data {xps} | R Documentation

## Import CEL files into a DataTreeSet

### Description

Import the Affymetrix CEL files into a ROOT file and create S4 class DataTreeSet

### Usage

    import.data(xps.scheme,
                filename = character(0),
                filedir  = getwd(),
                celdir   = NULL,
                celfiles = "*",
                celnames = NULL,
                project  = NULL,
                verbose  = TRUE)

### Arguments

`xps.scheme` | a `SchemeTreeSet` containing the correct scheme for the CEL-files
`filename` | file name of ROOT data file.
`filedir` | system directory where ROOT data file should be stored.
`celdir` | system directory containing the CEL-files for corresponding scheme.
`celfiles` | optional vector of CEL-files to be imported.
`celnames` | optional vector of names which should replace the CEL-file names.
`project` | optional class `ProjectInfo`.
`verbose` | logical, if `TRUE` print status information.

### Details

`import.data` is used to import CEL-files from directory `celdir` into a `ROOT` data file. To import only a subset of CEL-files, list these CEL-files as vector `celfiles`.

To import CEL-files from different directories, vector `celfiles` must contain the full path for each CEL-file and `celdir` must be `celdir=NULL`.

Currently, the following types of Affymetrix CEL-files can be imported: text (version 3), xml, binary (xda), generic (agcc,calvin)

An S4 class `DataTreeSet` will be created, serving as R wrapper to the `ROOT` data file `filename`.

Use function `root.data` to access the `ROOT` data file from new R sessions to avoid creating a new `ROOT` data file for every session.

### Value

A `DataTreeSet` object.

### Note

As mentioned above, use function `root.data` to access the ROOT data file from new R sessions to avoid creating a new `ROOT` data file for every R session.

Do not separate `filename` of ROOT files with dots, use underscores, e.g. do not use `filename="Data.Test3"` but use `filename="Data_Test3"` or `filename="DataTest3"` instead.

To every ROOT data file the extension “_cel” is attached to `filename` to easily recognize ROOT data files containing the raw CEL data, e.g. for `filename="Data_Test3"` the final name is “Data_Test3_cel.root”. Extension “root” is added automatically, so that ROOT is able to recognize the file as ROOT file.

Once a `ROOT` file is created it can not be overwritten, it must be deleted manually first. Only `ROOT` files called “tmp” or with `filename` starting with “tmp_” will be re-created automatically.

If CEL-file names contain dots and/or colons as characters, these characters will be replaced by underscores. It is recommended to use parameter `celnames` to create shorter CEL names and to replace special characters.

### Author(s)

Christian Stratowa

### See Also

`root.data`, `DataTreeSet`

### Examples

    ## get scheme and import CEL-files from package
    scheme.test3 <- root.scheme(paste(.path.package("xps"),"schemes/SchemeTest3.root",sep="/"))
    data.test3 <- import.data(scheme.test3,"tmp_data_test3",celdir=paste(.path.package("xps"),"raw",sep="/"))
    unlist(treeNames(data.test3))

    ## import only subset of CEL-files
    subdata.test3 <- import.data(scheme.test3,"tmpdt_data_test3",celdir=paste(.path.package("xps"),"raw",sep="/"),
                     celfiles=c("TestA1.CEL","TestB2.CEL"),verbose=FALSE)
    unlist(treeNames(subdata.test3))

[Package xps version 1.2.10 Index]