| ExprTreeSet-class {xps} | R Documentation |
This class provides the link to the ROOT expression file and
the ROOT trees contained therein. It extends class ProcesSet.
Objects are created using functions express, summarize
or normalize, or the specialized functions rma, mas5
or mas4.
exprtype:"character" representing the exression type,
i.e. ‘rma’, ‘mas5’, ‘mas4’ or ‘custom’.normtype:"character" representing the normalization
type, i.e. ‘mean’, ‘median’, ‘lowess’,‘supsmu’.scheme:"SchemeTreeSet" providing access to
ROOT scheme file.data:"data.frame". The data.frame can contain
the data (e.g. expression levels) stored in ROOT data trees.params:"list" representing relevant parameters.setname:"character" representing the name to the
ROOT file subdirectoy where the ROOT data trees are stored,
usually ‘PreprocesSet’.settype:"character" describing the type of treeset
stored in setname, usually ‘preprocess’.rootfile:"character" representing the name
of the ROOT data file, including full path.filedir:"character" describing the full path to
the system directory where rootfile is stored.numtrees:"numeric" representing the number of
ROOT trees stored in subdirectoy setname.treenames:"list" representing the names of the
ROOT trees stored in subdirectoy setname.
Class "ProcesSet", directly.
Class "TreeSet", by class "ProcesSet", distance 2.
signature(object = "ExprTreeSet"): exports expression trees from
ROOT expression file and and saves as data.frame data.signature(object = "ExprTreeSet"): extracts slot exprtype.signature(object = "ExprTreeSet", value = "character"): replaces slot exprtype.signature(object = "ExprTreeSet"): extracts the expression data.frame.signature(object = "ExprTreeSet", value = "data.frame"): replaces the expression data.frame.signature(x = "ExprTreeSet"): creates an MvA-plot.signature(object = "ExprTreeSet"): extracts slot normtype.signature(object = "ExprTreeSet", value = "character"): replaces slot normtype.signature(object = "ExprTreeSet"): replaces data.frame data
with an empty data.frame of dim(0,0).signature(object = "ExprTreeSet"): extracts the standard deviation data.frame.signature(object = "ExprTreeSet"): applies normalization methods.signature(object = "ExprTreeSet"): applies prefiltering methods.signature(object = "ExprTreeSet"): applies unifiltering methods.Christian Stratowa
related classes DataTreeSet, CallTreeSet.
showClass("ExprTreeSet")