DataTreeSet-class {xps} | R Documentation

## Class DataTreeSet

### Description

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

### Objects from the Class

Objects can be created using the functions `import.data` or `root.data`.

### Slots

`bgtreenames`:
  Object of class `"list"` representing the names of optional `ROOT` background trees.
`bgrd`:
  Object of class `"data.frame"`. The data.frame can contain background intensities stored in `ROOT` background trees.
`projectinfo`:
  Object of class `"ProjectInfo"` containing information about the project.
`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. intensities) 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 ‘DataTreeSet’.
`settype`:
  Object of class `"character"` describing the type of treeset stored in `setname`, usually ‘rawdata’.
`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

addData
  `signature(object = "DataTreeSet")`: import additional CEL-files and update `ROOT` data file `rootfile`.
attachBgrd
  `signature(object = "DataTreeSet")`: exports background trees from `ROOT` data file and and saves as data.frame `bgrd`.
attachInten
  `signature(object = "DataTreeSet")`: exports intensity trees from `ROOT` data file and and saves as data.frame `data`.
attachMask
  `signature(object = "DataTreeSet")`: exports scheme tree from `ROOT` scheme file and and saves as data.frame `mask` of slot `scheme`.
background
  `signature(object = "DataTreeSet")`: extracts slot `bgrd`.
background<-
  `signature(object = "DataTreeSet", value = "data.frame")`: replaces slot `bgrd`.
bgtreeNames
  `signature(object = "DataTreeSet")`: extracts slot `bgtreenames`.
image
  `signature(x = "DataTreeSet")`: creates an image for each column from data.frame `data` or `bgrd`, respectively.
intensity
  `signature(object = "DataTreeSet")`: extracts slot `data`.
intensity<-
  `signature(object = "DataTreeSet", value = "data.frame")`: replaces slot `data`.
mm
  `signature(object = "DataTreeSet")`: extracts the mismatch intensities.
ncols
  `signature(object = "DataTreeSet")`: extracts the physical number of array columns from slot `scheme`.
nrows
  `signature(object = "DataTreeSet")`: extracts the physical number of array rows from slot `scheme`.
pm
  `signature(object = "DataTreeSet")`: extracts the perfect match intensities.
pmplot
  `signature(x = "DataTreeSet")`: creates a barplot of mean perfect match and mismatch intensities.
projectInfo
  `signature(object = "DataTreeSet")`: extracts slot `projectinfo`.
projectInfo<-
  `signature(object = "DataTreeSet", value = "ProjectInfo")`: replaces slot `projectinfo`.
rawCELName
  `signature(object = "DataTreeSet")`: returns the name(s) of the imported raw CEL-files.
removeBgrd
  `signature(object = "DataTreeSet")`: replaces data.frame `bgrd` with an empty data.frame of dim(0,0).
removeInten
  `signature(object = "DataTreeSet")`: replaces data.frame `data` with an empty data.frame of dim(0,0).
removeMask
  `signature(object = "DataTreeSet")`: replaces data.frame `mask` from slot `scheme` with an empty data.frame of dim(0,0).
validBgrd
  `signature(object = "DataTreeSet")`: extracts the valid data from data.frame `bgrd`.
validData
  `signature(object = "DataTreeSet")`: extracts a subset of valid data from data.frame `data`.
xpsBgCorrect
  `signature(object = "DataTreeSet")`: applies background correction methods. See `bgcorrect`.
xpsDABGCall
  `signature(object = "DataTreeSet")`: computes DABG call.
xpsMAS4
  `signature(object = "DataTreeSet")`: computes MAS4 expression levels.
xpsMAS5
  `signature(object = "DataTreeSet")`: computes MAS5 expression levels.
xpsMAS5Call
  `signature(object = "DataTreeSet")`: computes MAS5 detection call.
xpsNormalize
  `signature(object = "DataTreeSet")`: applies normalization methods.
xpsPreprocess
  `signature(object = "DataTreeSet")`: applies normalization methods.
xpsRMA
  `signature(object = "DataTreeSet")`: computes RMA expression levels.
xpsSummarize
  `signature(object = "DataTreeSet")`: applies summarization methods.

### Author(s)

Christian Stratowa

### See Also

related classes `ExprTreeSet`, `CallTreeSet`.

### Examples

    showClass("DataTreeSet")

[Package xps version 1.0.2 Index]