import.exon.scheme {xps} | R Documentation

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

### Description

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

### Usage

    import.exon.scheme(filename   = character(0),
                       filedir    = getwd(),
                       layoutfile = character(0),
                       schemefile = character(0),
                       probeset   = character(0),
                       transcript = character(0),
                       control    = "",
                       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.
`probeset` | name of probeset annotation-file, including full path.
`transcript` | name of transcript annotation-file, including full path.
`control` | optional name of controls.ps-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.exon.scheme` is used to import all information for an Affymetrix exon array into a `ROOT` scheme file, including CLF and PGF-files, and the current Afymetrix probeset and 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’ should be able to import all Affymetrix exon array annotation files up to November 2008. However, since Affymetrix is still changing the headers and/or columns of the annotation files, future annotation files may require adaptation of the source code, thus the current version of ‘xps’ may not be able to read these files.

### 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.HuEx10stv2r2.na27"` but use `filename="Scheme_HuEx10stv2r2_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.expr.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 HuEx-1_0-st-v2.r2 Exon array
    scheme.huex10stv2r2.na27 <- import.exon.scheme("Scheme_HuEx10stv2r2_na27",filedir=scmdir,
                                layoutfile=paste(libdir,"HuEx-1_0-st-v2_libraryfile/HuEx-1_0-st-r2/HuEx-1_0-st-v2.r2.clf",sep="/"),
                                schemefile=paste(libdir,"HuEx-1_0-st-v2_libraryfile/HuEx-1_0-st-r2/HuEx-1_0-st-v2.r2.pgf",sep="/"),
                                probeset=paste(anndir,"HuEx-1_0-st-v2.na27.hg18.probeset.csv",sep="/"),
                                transcript=paste(anndir,"HuEx-1_0-st-v2.na27.hg18.transcript.csv",sep="/"))

    ## access ROOT scheme file from new R session
    scheme.huex10stv2r2 <- root.scheme(paste(scmdir,"Scheme_HuEx10stv2r2_na27.root",sep="/"))

    ## create scheme for HuGene-1_0-st-v1.r4 as exon array
    scheme.hugene10stv1r4.na27 <- import.exon.scheme("Scheme_HuGene10stv1r4_na27_2",filedir=scmdir,
                                  layoutfile=paste(libdir,"HuGene-1_0-st-v1.r4.analysis-lib-files/HuGene-1_0-st-v1.r4.clf",sep="/"),
                                  schemefile=paste(libdir,"HuGene-1_0-st-v1.r4.analysis-lib-files/HuGene-1_0-st-v1.r4.pgf",sep="/"),
                                  probeset=paste(anndir,"HuGene-1_0-st-v1.na27.2.hg18.probeset.csv",sep="/"),
                                  transcript=paste(anndir,"HuGene-1_0-st-v1.na27.hg18.transcript.csv",sep="/"))

    ## access ROOT scheme file from new R session
    scheme.hugene10stv1r4 <- root.scheme(paste(scmdir,"Scheme_HuGene10stv1r4_na27_2.root",sep="/"))

    ## create scheme for HuEx-1_0-st-v2.r2 Exon array with the old annotation file
    scheme.huex10stv2r2.old <- import.exon.scheme("Scheme_HuEx10stv2r2_old",filedir=scmdir,
                               layoutfile=paste(libdir,"HuEx-1_0-st-v2_libraryfile/HuEx-1_0-st-r2/HuEx-1_0-st-v2.r2.clf",sep="/"),
                               schemefile=paste(libdir,"HuEx-1_0-st-v2_libraryfile/HuEx-1_0-st-r2/HuEx-1_0-st-v2.r2.pgf",sep="/"),
                               probeset=paste(anndir,"HuEx-1_0-st-probeset-annot.csv",sep="/"),
                               transcript=paste(anndir,"HuEx-1_0-st-transcript-annot.csv",sep="/"),
                               control=paste(libdir,"HuEx-1_0-st-v2_libraryfile/HuEx-1_0-st-r2/HuEx-1_0-st-v2.r2.controls.ps",sep="/"))
    ## End(Not run)

[Package xps version 1.2.10 Index]