ExprTreeSet-class {xps} | R Documentation

## Class ExprTreeSet

### Description

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

### Objects from the Class

Objects are created using functions `express`, `summarize` or `normalize`, or the specialized functions `rma`, `mas5` or `mas4`.

### Slots

`exprtype`:
  Object of class `"character"` representing the exression type, i.e. ‘rma’, ‘mas5’, ‘mas4’ or ‘custom’.
`normtype`:
  Object of class `"character"` representing the normalization type, i.e. ‘mean’, ‘median’, ‘lowess’,‘supsmu’.
`scheme`:
  Object of class `"SchemeTreeSet"` providing access to `ROOT` scheme file.
`data`:
  Object of class `"data.frame"`. The data.frame can contain the data (e.g. expression levels) stored in `ROOT` data trees.
`params`:
  Object of class `"list"` representing relevant parameters.
`setname`:
  Object of class `"character"` representing the name to the `ROOT` file subdirectoy where the `ROOT` data trees are stored, usually ‘PreprocesSet’.
`settype`:
  Object of class `"character"` describing the type of treeset stored in `setname`, usually ‘preprocess’.
`rootfile`:
  Object of class `"character"` representing the name of the `ROOT` data 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 `"ProcesSet"`, directly. Class `"TreeSet"`, by class "ProcesSet", distance 2.

### Methods

attachExpr
  `signature(object = "ExprTreeSet")`: exports expression trees from `ROOT` expression file and and saves as data.frame `data`.
exprType
  `signature(object = "ExprTreeSet")`: extracts slot `exprtype`.
exprType<-
  `signature(object = "ExprTreeSet", value = "character")`: replaces slot `exprtype`.
exprs
  `signature(object = "ExprTreeSet")`: extracts the expression data.frame.
exprs<-
  `signature(object = "ExprTreeSet", value = "data.frame")`: replaces the expression data.frame.
mvaplot
  `signature(x = "ExprTreeSet")`: creates an MvA-plot.
normType
  `signature(object = "ExprTreeSet")`: extracts slot `normtype`.
normType<-
  `signature(object = "ExprTreeSet", value = "character")`: replaces slot `normtype`.
removeExpr
  `signature(object = "ExprTreeSet")`: replaces data.frame `data` with an empty data.frame of dim(0,0).
se.exprs
  `signature(object = "ExprTreeSet")`: extracts the standard deviation data.frame.
xpsNormalize
  `signature(object = "ExprTreeSet")`: applies normalization methods.
xpsPreFilter
  `signature(object = "ExprTreeSet")`: applies prefiltering methods.
xpsUniFilter
  `signature(object = "ExprTreeSet")`: applies unifiltering methods.

### Author(s)

Christian Stratowa

### See Also

related classes `DataTreeSet`, `CallTreeSet`.

### Examples

    showClass("ExprTreeSet")

[Package xps version 1.4.10 Index]