ExprTreeSet-class: Class ExprTreeSet

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

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.

corplot

signature(x = "ExprTreeSet"): creates a correlation heat map.

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.

madplot

signature(x = "ExprTreeSet"): creates a false color display of between arrays distances.

mvaplot

signature(x = "ExprTreeSet"): creates an MvA-plot.

normType

signature(object = "ExprTreeSet"): extracts slot normtype.

normType<-

signature(object = "ExprTreeSet", value = "character"): replaces slot normtype.

nuseplot

signature(x = "ExprTreeSet"): creates a NUSE-plot.

pcaplot

signature(x = "ExprTreeSet"): plots first two principal components of PCA.

rleplot

signature(x = "ExprTreeSet"): creates a RLE-plot.

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.

validExpr

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

validSE

signature(object = "ExprTreeSet"): extracts data columns from data.frame se.exprs.

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, QualTreeSet.

Examples

showClass("ExprTreeSet")

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