QualTreeSet-class: Class QualTreeSet
Description
This class provides the link to the ROOT quality control file and
the ROOT trees contained therein. It extends class ProcesSet.Slots
qualopt:- Object of class
"character" representing the quality control option,
i.e. ‘raw’, ‘adjusted’, ‘normalized’ or ‘all’. qualtype:- Object of class
"character" representing the quality control type,
i.e. ‘rlm’. 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
- borderplot
signature(x = "QualTreeSet"): creates a boxplot of positive and
negative border elements.- borders
signature(object = "QualTreeSet"): exports border trees from
ROOT quality control file as data.frame data.- coiplot
signature(x = "QualTreeSet"): creates a Center-of-Intensity-plot for
positive and negative feature intensities.- image
signature(x = "QualTreeSet"): creates a pseudo image for each quality
control tree, i.e. residual images.- NUSE
signature(x = "QualTreeSet"): plot Normalized Unscaled Standard Errors, or return stats, values.- nuseplot
signature(x = "QualTreeSet"): creates a NUSE-plot.- qualOption
signature(object = "QualTreeSet"): extracts slot qualopt.- qualOption<-
signature(object = "QualTreeSet", value = "character"): replaces slot qualopt.- qualType
signature(object = "QualTreeSet"): extracts slot qualtype.- qualType<-
signature(object = "QualTreeSet", value = "character"): replaces slot qualtype.- residuals
signature(object = "QualTreeSet"): exports residuals from the
residuals trees of the ROOT quality control file as data.frame data.- RLE
signature(x = "QualTreeSet"): plot Relative Log Expression, or return stats, values.- rleplot
signature(x = "QualTreeSet"): creates a RLE-plot.- weights
signature(object = "QualTreeSet"): exports weights from the
residuals trees of the ROOT quality control file as data.frame data.- xpsRNAdeg
signature(x = "QualTreeSet"): list with parameters for RNA degradation.
See Also
related classes DataTreeSet, CallTreeSet, ExprTreeSet.