CallTreeSet-class: Class CallTreeSet

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 call file and the ROOT trees contained therein. It extends class ProcesSet.

Objects from the Class

Objects are created using functions mas5.call or dabg.call, respectively.

Slots

calltype:

Object of class "character" representing the call type, i.e. ‘mas5’ or ‘dabg’.

detcall:

Object of class "data.frame". The data.frame can contain the detection calls stored in ROOT call trees.

scheme:

Object of class "SchemeTreeSet" providing access to ROOT scheme file.

data:

Object of class "data.frame". The data.frame can contain the data (i.e. p-values) stored in ROOT call 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 call trees are stored, usually ‘CallTreeSet’.

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 call 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

attachCall

signature(object = "CallTreeSet"): exports detection call data from ROOT call file and and saves as data.frame detcall.

attachPVal

signature(object = "CallTreeSet"): exports call p-values from ROOT call file and and saves as data.frame data.

callplot

signature(x = "CallTreeSet"): creates a barplot of percent present and absent calls.

presCall

signature(object = "CallTreeSet"): extracts the detection call data.frame.

presCall<-

signature(object = "CallTreeSet", value = "data.frame"): replaces the detection call data.frame.

pvalData

signature(object = "CallTreeSet"): extracts the detection p-value data.frame.

pvalData<-

signature(object = "CallTreeSet", value = "data.frame"): replaces the detection p-value data.frame.

removeCall

signature(object = "CallTreeSet"): replaces data.frame detcall with an empty data.frame of dim(0,0).

removePVal

signature(object = "CallTreeSet"): replaces data.frame data with an empty data.frame of dim(0,0).

validCall

signature(object = "CallTreeSet"): extracts a subset of columns from data.frame detcall.

validPVal

signature(object = "CallTreeSet"): extracts a subset of columns from data.frame data.

Author(s)

Christian Stratowa

See Also

related classes DataTreeSet, ExprTreeSet.

Examples

showClass("CallTreeSet")

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