ProcesSet-class: Class ProcesSet

In xps: Processing and Analysis of Affymetrix Oligonucleotide Arrays including Exon Arrays, Whole Genome Arrays and Plate Arrays

Description

This class provides access to class SchemeTreeSet for the derived classes DataTreeSet, ExprTreeSet and CallTreeSet. It extends class TreeSet.

Objects from the Class

Usually, no objects are created from it.

Slots

scheme:

Object of class "SchemeTreeSet" providing access to ROOT scheme file.

data:

Object of class "data.frame". The data.frame can contain the data 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 trees are stored, usually one of ‘DataTreeSet’, ‘PreprocesSet’, ‘CallTreeSet’.

settype:

Object of class "character" describing the type of treeset stored in setname, usually one of ‘rawdata’, ‘preprocess’.

rootfile:

Object of class "character" representing the name of the ROOT 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

attachData

signature(object = "ProcesSet"): exports data from ROOT data file and and saves as data.frame data.

boxplot

signature(x = "ProcesSet"): creates a boxplot of the data from data.frame data.

chipName

signature(object = "ProcesSet"): extracts slot chipname from slot scheme.

chipType

signature(object = "ProcesSet"): extracts slot chiptype from slot scheme.

export

signature(object = "ProcesSet"): exports ROOT trees as text file, see export-methods.

getTreeData

signature(object = "ProcesSet"): exports tree data from ROOT file rootfile, and saves as data.frame data.

hist

signature(x = "ProcesSet"): creates a plot showing the histograms for data.frame data.

image

signature(x = "ProcesSet"): creates an image for each column from data.frame data or bgrd, respectively.

mboxplot

signature(x = "ProcesSet"): creates an M-boxplot of the data from data.frame data.

removeData

signature(object = "ProcesSet"): replaces data.frame data with an empty data.frame of dim(0,0).

schemeFile

signature(object = "ProcesSet"): extracts the ROOT scheme file from slot scheme.

schemeFile<-

signature(object = "ProcesSet"), value = "character"): replaces the ROOT scheme file from slot scheme.

schemeSet

signature(object = "ProcesSet"): extracts slot scheme.

schemeSet<-

signature(object = "ProcesSet"), value = "SchemeTreeSet"): replaces slot scheme with a different SchemeTreeSet.

treeData

signature(object = "ProcesSet"): extracts all columns from data.frame data.

validData

signature(object = "ProcesSet"): extracts a subset of columns from data.frame data.

Author(s)

Christian Stratowa

See Also

derived classes DataTreeSet, ExprTreeSet, CallTreeSet, QualTreeSet.

Examples

showClass("ProcesSet")

xps documentation built on Nov. 8, 2020, 6 p.m.