SchemeTreeSet-class {xps} | R Documentation

## Class SchemeTreeSet

### Description

This class provides the link to the `ROOT` scheme file and the `ROOT` trees contained therein. It extends class `TreeSet`.

### Objects from the Class

Objects can be created using the functions `import.expr.scheme`, `import.exon.scheme`, `import.genome.scheme` or `root.scheme`.

### Slots

`chipname`:
  Object of class `"character"` representing the Affymetrix chip name.
`chiptype`:
  Object of class `"character"` representing the chip tpye, either ‘GeneChip’, ‘GenomeChip’ or ‘ExonChip’.
`probeinfo`:
  Object of class `"list"` representing chip information, including nrows, ncols, number of probes, etc.
`mask`:
  Object of class `"data.frame"`. The data.frame can contain the mask used to identify the probes as e.g. PM, MM or control probes.
`setname`:
  Object of class `"character"` representing the name to the `ROOT` file subdirectoy where the `ROOT` scheme trees are stored; it is identical to `chipname`.
`settype`:
  Object of class `"character"` describing the type of treeset stored in `setname`, i.e. ‘scheme’.
`rootfile`:
  Object of class `"character"` representing the name of the `ROOT` scheme file, including full path.
`filedir`:
  Object of class `"character"` describing the full path to the system directory where `rootfile` is stored.
`numtrees`:
  Object of class `"numeric"` representing the number of `ROOT` trees stored in subdirectoy `setname`.
`treenames`:
  Object of class `"list"` representing the names of the `ROOT` trees stored in subdirectoy `setname`.

### Extends

Class `"TreeSet"`, directly.

### Methods

attachMask
  `signature(object = "SchemeTreeSet")`: exports scheme tree from `ROOT` scheme file and and saves as data.frame `mask`.
chipMask
  `signature(object = "SchemeTreeSet")`: extracts data.frame `mask`.
chipMask<-
  `signature(object = "SchemeTreeSet", value = "data.frame")`: replaces data.frame `mask`.
chipName
  `signature(object = "SchemeTreeSet")`: extracts slot `chipname`.
chipType
  `signature(object = "SchemeTreeSet")`: extracts slot `chiptype`.
chipType<-
  `signature(object = "SchemeTreeSet", value = "character")`: replaces slot `chiptype`.
export
  `signature(object = "SchemeTreeSet")`: exports `ROOT` trees as text file, see `export-methods`.
ncols
  `signature(object = "SchemeTreeSet")`: extracts the physical number of array columns from slot `probeinfo`.
nrows
  `signature(object = "SchemeTreeSet")`: extracts the physical number of array rows from slot `probeinfo`.
probeInfo
  `signature(object = "SchemeTreeSet")`: extracts slot `probeinfo`.
removeMask
  `signature(object = "SchemeTreeSet")`: replaces data.frame `mask` with an empty data.frame of dim(0,0).

### Author(s)

Christian Stratowa

### Examples

    showClass("SchemeTreeSet")

[Package xps version 1.4.10 Index]