export {xps} | R Documentation

## Export data as text files

### Description

Export data from classes `SchemeTreeSet`, `DataTreeSet`, `ExprTreeSet`, or `CallTreeSet` to `outfile`.

### Usage

    export.scheme(xps.scheme, treetype = character(0), varlist = "*", outfile = character(0), sep = "\t", as.dataframe = FALSE, verbose = TRUE)

    export.data(xps.data, treename = "*", treetype = "cel", varlist = "*", outfile = character(0), sep = "\t", as.dataframe = FALSE, verbose = TRUE)

    export.expr(xps.expr, treename = "*", treetype = character(0), varlist = "*", outfile = character(0), sep = "\t", as.dataframe = FALSE, verbose = TRUE)

    export.call(xps.call, treename = "*", treetype = character(0), varlist = "*", outfile = character(0), sep = "\t", as.dataframe = FALSE, verbose = TRUE)

    export(object, ...)

### Arguments

`xps.scheme` | an object of type `SchemeTreeSet`.
`xps.data` | an object of type `DataTreeSet`.
`xps.expr` | an object of type `ExprTreeSet`.
`xps.call` | an object of type `CallTreeSet`.
`treename` | vector of tree names to export.
`treetype` | type of tree(s) to export, see `validTreetype`
`varlist` | names of tree leaves to export
`outfile` | name of output file.
`sep` | column separator
`as.dataframe` | if `TRUE` a data.frame will be returned.
`verbose` | logical, if `TRUE` print status information.
`object` | object of class `DataTreeSet`.
`...` | arguments `treenames`,`treetype`,`varlist`,`outfile`,`sep`,`as.dataframe`.

### Details

Export data from classes `SchemeTreeSet`, `DataTreeSet`, `ExprTreeSet`, or `CallTreeSet` to `outfile`.

Parameter `varlist` lists the parameters to export:
- parameters are separated by ":", e.g. `varlist="fInten:fStdev"`.
- for `varlist="*"` all valid parameters will be exported.

For class `DataTreeSet` the following `varlist` parameters are valid:

| `fInten`: | intensities from e.g. tree.cel.
| `fStdev`: | standard deviation from e.g. tree.cel.
| `fNPixels`: | number of pixels from e.g. tree.cel.
| `fBg`: | background values (background trees only).

For classes `ExprTreeSet` and `CallTreeSet` `varlist` can contain annotation parameters and parameters of the resulting data.
Following `varlist` annotation parameters are valid:

| `fUnitName`: | unit name (probeset ID).
| `fTranscriptID`: | transcript_id (probeset ID).
| `fName`: | gene name.
| `fSymbol`: | gene symbol.
| `fAccession`: | mRNA accession such as Refseq ID.
| `fEntrezID`: | entrez ID.
| `fChromosome`: | chromosome.
| `fStart`: | start position.
| `fStop`: | stop position.
| `fStrand`: | strand on chromosome.
| `fCytoBand`: | cytoband.

Following `varlist` parameters are valid for `ExprTreeSet`:

| `fLevel`: | expression level.
| `fStdev`: | standard deviation.
| `fNPairs`: | number of pairs.

Following `varlist` parameters are valid for `CallTreeSet`:

| `fCall`: | detection call.
| `fPValue`: | detection p-value.

An example: `varlist="fUnitName:fName:fSymbol:fLevel:fStdev:fEntrezID"`

`export` is a generic method to export data from `ROOT` trees as text file.

### Value

If `as.dataframe` is `TRUE`, the data will be imported into the current R session as `data.frame`. Otherwise, `NULL` will be returned.

### Author(s)

Christian Stratowa

### See Also

`export-methods`

### Examples

    ## load existing ROOT scheme file and ROOT data file
    scheme.test3 <- root.scheme(paste(.path.package("xps"),"schemes/SchemeTest3.root",sep="/"))
    data.test3 <- root.data(scheme.test3, paste(.path.package("xps"),"rootdata/DataTest3_cel.root",sep="/"))

    ## export as table only
    export(scheme.test3, treetype="idx", outfile="Test3_idx.txt",verbose=FALSE)

    ## export as table and import as data.frame
    ann <- export.scheme(scheme.test3, treetype="ann", outfile="Test3_ann.txt",as.dataframe=TRUE,verbose=FALSE)
    head(ann)
    data <- export.data(data.test3, outfile="Test3_cel.txt",as.dataframe=TRUE,verbose=FALSE)
    head(data)

[Package xps version 1.2.10 Index]