import.genome.scheme {xps} | R Documentation

## Import CLF, PGF and annotation files into a SchemeTreeSet

### Description

Import the Affymetrix CLF, PGF and transcript annotation files into a ROOT file and create S4 class SchemeTreeSet

### Usage

    import.genome.scheme(filename   = character(0),
                         filedir    = getwd(),
                         layoutfile = character(0),
                         schemefile = character(0),
                         transcript = character(0),
                         add.mask   = FALSE,
                         verbose    = TRUE)

### Arguments

`filename` | file name of ROOT scheme file.
`filedir` | system directory where ROOT scheme file should be stored.
`layoutfile` | name of CLF-file, including full path.
`schemefile` | name of PGF-file, including full path.
`transcript` | name of transcript annotation-file, including full path.
`add.mask` | logical. If `TRUE` mask information will be included as slot `mask`.
`verbose` | logical, if `TRUE` print status information.

### Details

`import.genome.scheme` is used to import all information for an Affymetrix whole genome array into a `ROOT` scheme file, including CLF and PGF-files, and the current Afymetrix transcript annotation files.

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

Since a new `ROOT` scheme file needs only to be created when new annotation files are available from the Affymetrix website, it is recommended to store all `ROOT` scheme files in a commonly accessible system directory `filedir`.

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

### Value

A `SchemeTreeSet` object.

### Warning

The current version of ‘xps’ is able to import all Affymetrix genome array annotation files up to November 2008, i.e. all files of release 3 (r3) and earlier. However, in January 2009 Affymetrix has updated all CLF, PGF and annotation files to release 4 (r4) and added a new probeset annotation file, thus in effect changing the whole genome arrays to exon arrays!

Thus, for release 4 (r4) files, function `import.genome.scheme` can no longer be used, but you must use function `import.exon.scheme` instead (see examples).

### Note

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

Do not separate `filename` of ROOT files with dots, use underscores, e.g. do not use `filename="Scheme.HuGene10stv1.na27"` but use `filename="Scheme_HuGene10stv1_na27"` instead. Extension “root” is added automatically, so that ROOT is able to recognize the file as ROOT file.

Do not set `add.mask=TRUE` unless you know that your computer has sufficient RAM.

Do not add item `control` unless you want to use one of the old annotation files where the probeset annotation file does not contain the AFFX controls.

### Author(s)

Christian Stratowa

### See Also

`import.exon.scheme`, `root.scheme`, `SchemeTreeSet`

### Examples

    ## Not run:
    ## define paths
    scmdir <- "/common/path/schemes"
    libdir <- "/my/path/Affy/libraryfiles"
    anndir <- "/my/path/Affy/Annotation"

    ## create scheme for HuGene-1_0-st-v1 whole genome array
    scheme.hugene10stv1r3.na27 <- import.genome.scheme("Scheme_HuEx10stv1r3_na27",filedir=scmdir,
                                  layoutfile=paste(libdir,"HuGene-1_0-st-v1.r3.analysis_libraryfile/HuGene-1_0-st-v1.r3.clf",sep="/"),
                                  schemefile=paste(libdir,"HuGene-1_0-st-v1.r3.analysis_libraryfile/HuGene-1_0-st-v1.r3.pgf",sep="/"),
                                  transcript=paste(anndir,"HuGene-1_0-st-v1.na27.hg18.transcript.csv",sep="/"))

    ## access ROOT scheme file from new R session
    scheme.hugene10stv1r3 <- root.scheme(paste(scmdir,"Scheme_HuEx10stv1r3_na27.root",sep="/"))
    ## End(Not run)

[Package xps version 1.4.10 Index]