ExprTreeSet-class: Class ExprTreeSet
Description
This class provides the link to the ROOT expression file and
the ROOT trees contained therein. It extends class ProcesSet.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.
See Also
related classes DataTreeSet, CallTreeSet, QualTreeSet.