validTreetype {xps} | R Documentation

## Validate Tree Type

### Description

Validate tree type for corresponding data type.

### Usage

    validTreetype(treetype, datatype)

### Arguments

`treetype` | tree type.
`datatype` | data type.

### Details

Every `ROOT` tree has an extension, which describes the type of data stored in this tree. For example, ‘TestA1.cel’ is the tree name that stores the CEL-file data for ‘TestA1.CEL’.

Trees with `datatype="scheme"` have the following extensions:
`scm`: scheme tree containing (x,y)-coordinates and mask for UNIT_ID.
`idx`: unit tree containing UnitName (i.e. probeset id), NumCells, NumAtoms, UnitType, for UNIT_ID.
`prb`: probe tree containing probe sequences.
`ann`: transcript annotation tree.
`anx`: exon annotation tree; exon arrays only.
`anp`: probeset annotation tree; exon arrays only.
`cxy`: coordinate tree containing CLF-file information; exon arrays only.
`exn`: exon tree; exon arrays only.
`pbs`: probeset tree; exon arrays only.

Trees with `datatype="rawdata"` have the following extensions:
`cel`: data tree containing CEL-file data.

Trees with `datatype="preprocess"` have the following extensions:
`int`: intensity tree containing background-corrected intensities.
`sbg`: background tree containing MAS4 sector background levels.
`wbg`: background tree containing MAS5 weighted sector background levels.
`rbg`: background tree containing RMA background levels.
`gbg`: background tree containing GC-content background levels.
`cmn`: cell tree containing preprocessed intensities using algorithm ‘mean’.
`cmd`: cell tree containing preprocessed intensities using algorithm ‘median’.
`clw`: cell tree containing preprocessed intensities using algorithm ‘lowess’.
`css`: cell tree containing preprocessed intensities using algorithm ‘supsmu’.
`cqu`: cell tree containing preprocessed intensities using algorithm ‘quantile’.
`dc5`: detection tree containing MAS5 detection call and p-value.
`dab`: detection tree containing DABG detection call and p-value.
`amn`: expression tree containing expression levels computed with ‘arithmetic mean’.
`gmn`: expression tree containing expression levels computed with ‘geometric mean’.
`wmn`: expression tree containing expression levels computed with ‘weighted mean’.
`wdf`: expression tree containing expression levels computed with ‘weighted difference’.
`adf`: expression tree containing expression levels computed with ‘average difference’.
`tbw`: expression tree containing expression levels computed with ‘tukey biweight’.
`mdp`: expression tree containing expression levels computed with ‘median polish’.

Trees with `datatype="normation"` have the following extensions:
`tmn`: expression tree after normalization using algorithm ‘trimmed mean’.
`med`: expression tree after normalization using algorithm ‘median’.
`ksm`: expression tree after normalization using algorithm ‘kernel smoother’.
`low`: expression tree after normalization using algorithm ‘lowess’.
`sup`: expression tree after normalization using algorithm ‘supsmu’.
`qua`: expression tree after normalization using algorithm ‘quantile’.
`mdp`: expression tree after normalization using algorithm ‘median polish’.

### Value

Returns the valid `treetype`, otherwise an error message is returned.

### Note

Not all tree types are used in the current package.

### Author(s)

Christian Stratowa

### See Also

`getDatatype`, `type2Exten`

### Examples

    validTreetype("prb", "scheme")
    validTreetype("cel", "rawdata")
    validTreetype("tbw", "preprocess")

[Package xps version 1.2.10 Index]