DataTreeSet-class {xps} | R Documentation |
This class provides the link to the ROOT
data file and
the ROOT
trees contained therein. It extends class ProcesSet
.
Objects can be created using the functions import.data
or root.data
.
bgtreenames
:"list"
representing the names of
optional ROOT
background trees.bgrd
:"data.frame"
. The data.frame can contain
background intensities stored in ROOT
background trees.projectinfo
:"ProjectInfo"
containing information
about the project.scheme
:"SchemeTreeSet"
providing access to
ROOT
scheme file.data
:"data.frame"
. The data.frame can contain
the data (e.g. intensities) 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 ‘DataTreeSet’.settype
:"character"
describing the type of treeset
stored in setname
, usually ‘rawdata’.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 = "DataTreeSet")
: import additional CEL-files and
update ROOT
data file rootfile
.signature(object = "DataTreeSet")
: exports background trees from
ROOT
data file and and saves as data.frame bgrd
.signature(object = "DataTreeSet")
: exports intensity trees from
ROOT
data file and and saves as data.frame data
.signature(object = "DataTreeSet")
: exports scheme tree from
ROOT
scheme file and and saves as data.frame mask
of slot scheme
.signature(object = "DataTreeSet")
: extracts slot bgrd
.signature(object = "DataTreeSet", value = "data.frame")
: replaces slot bgrd
.signature(object = "DataTreeSet")
: extracts slot bgtreenames
.signature(x = "DataTreeSet")
: creates an image for each column from
data.frame data
or bgrd
, respectively.signature(object = "DataTreeSet")
: extracts slot data
.signature(object = "DataTreeSet", value = "data.frame")
: replaces slot data
.signature(object = "DataTreeSet")
: extracts the mismatch intensities.signature(object = "DataTreeSet")
: extracts the physical number of
array columns from slot scheme
.signature(object = "DataTreeSet")
: extracts the physical number of
array rows from slot scheme
.signature(object = "DataTreeSet")
: extracts the perfect match intensities.signature(x = "DataTreeSet")
: creates a barplot of mean perfect match and
mismatch intensities.signature(object = "DataTreeSet")
: extracts slot projectinfo
.signature(object = "DataTreeSet", value = "ProjectInfo")
: replaces slot projectinfo
.signature(object = "DataTreeSet")
: returns the name(s) of the
imported raw CEL-files.signature(object = "DataTreeSet")
: replaces data.frame bgrd
with an empty data.frame of dim(0,0).signature(object = "DataTreeSet")
: replaces data.frame data
with an empty data.frame of dim(0,0).signature(object = "DataTreeSet")
: replaces data.frame mask
from slot scheme
with an empty data.frame of dim(0,0).signature(object = "DataTreeSet")
: extracts the valid data
from data.frame bgrd
.signature(object = "DataTreeSet")
: extracts a subset of valid data
from data.frame data
.signature(object = "DataTreeSet")
: applies background correction methods.
See bgcorrect
.signature(object = "DataTreeSet")
: computes DABG call.signature(object = "DataTreeSet")
: computes I/NI call.signature(object = "DataTreeSet")
: computes MAS4 expression levels.signature(object = "DataTreeSet")
: computes MAS5 expression levels.signature(object = "DataTreeSet")
: computes MAS5 detection call.signature(object = "DataTreeSet")
: applies normalization methods.signature(object = "DataTreeSet")
: applies normalization methods.signature(object = "DataTreeSet")
: computes RMA expression levels.signature(object = "DataTreeSet")
: applies summarization methods.Christian Stratowa
related classes ExprTreeSet
, CallTreeSet
.
showClass("DataTreeSet")