track.CNV-class: Class '"track.CNV"'

In Rgb: The R Genome Browser

Class "track.CNV"

Description

This class is a variation of the track.table class dedicated to constitutive Copy Number Variations, enforcing new drawing parameter defaults and a few specialized methods.

Objects can be created by two distincts means :

• Using the corresponding constructors, which work like the track.table constructor.

• Importing a track.table object in an empty object created by a call to new.

Extends

Class track.table, directly.
Class refTable, by class track.table, distance 2.
Class crossable, by class track.table, distance 2.
Class sliceable, by class track.table, distance 3.
Class drawable, by class track.table, distance 4.

All reference classes extend and inherit methods from envRefClass.

Fields

The following fields are inherited (from the corresponding class):

• assembly (track.table)

• checktrack (track.table)

• colCount (refTable)

• colIterator (refTable)

• colNames (refTable)

• colReferences (refTable)

• index (track.table)

• name (drawable)

• organism (track.table)

• parameters (drawable)

• rowCount (refTable)

• rowNamed (refTable)

• rowNames (refTable)

• sizetrack (track.table)

• subtrack (track.table)

• values (refTable)

Methods

The following methods are inherited (from the corresponding class):

• addArms (track.table)

• addColumn (track.table)

• addDataFrame (refTable)

• addEmptyRows (refTable)

• addList (track.table)

• addVectors (refTable)

• buildCalls (track.table)

• buildGroupPosition (track.table)

• buildGroupSize (track.table)

• buildIndex (track.table)

• callParams (drawable)

• callSuper (envRefClass)

• check (track.table)

• chromosomes (track.table)

• coerce (track.table)

• colOrder (refTable)

• copy (refTable)

• cross (crossable)

• defaultParams (track.table, overloaded)

• delColumns (track.table)

• draw (sliceable)

• erase (refTable)

• eraseArms (track.table)

• export (envRefClass)

• extract (refTable)

• field (envRefClass)

• fill (track.table)

• fix.param (drawable)

• getChromEnd (track.table)

• getClass (envRefClass)

• getColCount (refTable)

• getColNames (refTable)

• getLevels (refTable)

• getName (drawable)

• getParam (drawable)

• getRefClass (envRefClass)

• getRowCount (refTable)

• getRowNames (refTable)

• import (envRefClass)

• indexes (refTable)

• initFields (envRefClass)

• initialize (track.table)

• isArmed (track.table)

• metaFields (track.table)

• rowOrder (track.table)

• segMerge (track.table)

• segOverlap (track.table)

• setColNames (track.table)

• setLevels (track.table)

• setName (drawable)

• setParam (drawable)

• setRowNames (refTable)

• show (track.table, overloaded)

• size (track.table)

• slice (track.table)

• trace (envRefClass)

• types (refTable)

• untrace (envRefClass)

• usingMethods (envRefClass)

Author(s)

Sylvain Mareschal

See Also

track.table-class, track.table, track.table.GTF

track.CNV, track.CNV.DGV

Rgb documentation built on Aug. 18, 2023, 5:05 p.m.