QualTreeSet-class: Class QualTreeSet

In xps: Processing and Analysis of Affymetrix Oligonucleotide Arrays including Exon Arrays, Whole Genome Arrays and Plate Arrays

Description

This class provides the link to the ROOT quality control file and the ROOT trees contained therein. It extends class ProcesSet.

Objects from the Class

Objects are created using functions qualify, fitQC, or the specialized functions qualify.rlm, fitRLM or rmaPLM.

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.

Author(s)

Christian Stratowa

See Also

related classes DataTreeSet, CallTreeSet, ExprTreeSet.

Examples

showClass("QualTreeSet")

xps documentation built on Nov. 8, 2020, 6 p.m.