| 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")