cghRA.design-class: Class '"cghRA.design"'

In cghRA: Array CGH Data Analysis and Visualization

Description

This class is part of the cghRA.array class. A single object from this class is used to store informations about probes for series of arrays sharing the same CGH design, in order to store only array-specific values in the array variables.

Objects from this class can be produced by the cghRA.design, Agilent.design and custom.design constructors. Alternatively they can be produced by the interactive function tk.design, included in tk.cghRA.

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

bias(...):

Computes the Waves aCGH Correction Algorithm (Lepretre et al. 2009) bias for the current design.
- ... : arguments to be passed to the bias() function (except from 'probeChrom', 'probeStarts' and 'probeEnds').

remap(...):

Recomputes the coordinates of the probes from the probes and genome sequences. Forces 'chrom' to factor, keeping levels if available.
- ... : arguments to be passed to the localize() function.

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, overloaded)

• 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, overloaded)

• 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

cghRA.design, Agilent.design, custom.design, tk.design

cghRA.array-class, refTable-class

cghRA documentation built on May 2, 2019, 3:34 a.m.