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.
xpsINICall
signature(object = "DataTreeSet"): computes I/NI 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 1.2.10 Index]