import.expr.scheme {xps} | R Documentation

## Import CDF, probe and annotation files into a SchemeTreeSet

### Description

Import the Affymetrix CDF, probe and annotation files into a ROOT file and create S4 class SchemeTreeSet

### Usage

    import.expr.scheme(filename   = character(0),
                       filedir    = getwd(),
                       schemefile = character(0),
                       probefile  = character(0),
                       annotfile  = character(0),
                       chipname   = NULL,
                       add.mask   = FALSE,
                       verbose    = TRUE)

### Arguments

`filename` | file name of ROOT scheme file.
`filedir` | system directory where ROOT scheme file should be stored.
`schemefile` | name of CDF-file, including full path.
`probefile` | name of probe-file, including full path.
`annotfile` | name of annotation-file, including full path.
`chipname` | optional chip name when using an alternative CDF-file.
`add.mask` | logical. If `TRUE` mask information will be included as slot `mask`.
`verbose` | logical, if `TRUE` print status information.

### Details

`import.expr.scheme` is used to import all information for an Affymetrix expression array into a `ROOT` scheme file, including CDF-file, the corresponding probe file, and the current Afymetrix annotation file.

Usually, `chipname` is extracted from the name of the CDF-file, however, when using an alternative CDF-file, e.g. from BrainArray or AffyProbeMiner, a `chipname` must be supplied which starts with (or contains) the exact Affymetrix chip name.

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 a new annotation file is 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.

### 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.Test3.na21"` but use `filename="Scheme_Test3_na21"` or simply `filename="SchemeTest3na21"` instead. Extension “root” is added automatically, so that ROOT is able to recognize the file as ROOT file.

For a few probesets, parsing the Affymetrix annotation files will provide ambiguous results. Setting `verbose=11` will list these probesets.

### Author(s)

Christian Stratowa

### See Also

`import.exon.scheme`, `import.genome.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 Test3 GeneChip
    scheme.test3.na22 <- import.expr.scheme("Scheme_Test3_na22",filedir=scmdir,
                         schemefile=paste(libdir,"Test3.CDF",sep="/"),
                         probefile=paste(libdir,"Test3_probe.tab",sep="/"),
                         annotfile=paste(anndir,"Test3.na22.annot.csv",sep="/"))

    ## access ROOT scheme file from new R session
    scheme.test3 <- root.scheme(paste(scmdir,"Scheme_Test3_na22.root",sep="/"))

    ## create scheme for HG-U133_Plus_2 GeneChip
    scheme.hgu133p2.na22 <- import.expr.scheme("Scheme_HGU133p2_na22",filedir=scmdir,
                            schemefile=paste(libdir,"HG-U133_Plus_2.cdf",sep="/"),
                            probefile=paste(libdir,"HG-U133-PLUS_probe.tab",sep="/"),
                            annotfile=paste(anndir,"HG-U133_Plus_2.na22.annot.csv",sep="/"))
    ## access ROOT scheme file from new R session
    scheme.hgu133p2 <- root.scheme(paste(scmdir,"Scheme_HGU133p2_na22.root",sep="/"))
    ## End(Not run)

[Package xps version 1.0.2 Index]