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")