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

In cghRA: Array CGH Data Analysis and Visualization

Description

This class is intended to store a list of genomic segments produced by a segmentation algorithm, with a mean log-ratio for each segment.

Objects from this class are intended to be produced by the DNAcopy method of the cghRA.array class, or the cghRA.regions constructor. Producing such objects is part of the process function and its interfaced version tk.process, found 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

model:

Numeric vector, storing the parameters and fitness of a copy-number model. See model.auto for further details on the components.

modelizeCall:

The R call which produced the stored copy-number model.

segmentCall:

The R call which produced the segments stored in the object.

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

fillGaps(...):

Apply the fillGaps() function to extend regions in order to fill inter-segment gaps.

karyotype(bandTrack, value = , thresholds = , precision = ):

Returns a karyotype formula of altered regions.
- bandTrack : a track.table object, as returned by track.UCSC_bands().
- value : column to use to select altered regions.
- thresholds : length 2 numeric vector defining altered values.
- precision : single integer value from 1 to 4, amount of digits to consider in banding.

model.apply(...):

Call the model.apply() function to produce a cghRA.copies object with predicted copy number for each region.

model.auto(save = , ...):

Call the model.auto() function to automatically fit a copy-number prediction model.
- save : single logical value, whether to save the model or only return it

modelized():

Does the object embed a complete model or not

model.test(...):

Call the model.test() function to plot the current copy-number model.

proportions(chrom = , value = , states = , mode = ):

Returns the proportion of the chromosomes in given states (in bp involved).
- chrom : character vector, chromosome location of the regions to query. Consider track.table$eraseArms() to focus on chromosome arms.
- value : single character value, name of the column to use for state assignation.
- states : list of states, see penetrance help page for details.

status(chrom, start, end, value = , na = , fuzzy = , states = ):

Returns the copy states in various windows, mimicing penetrance behavior.
- chrom : character vector, chromosome location of the regions to query.
- start : integer vector, starting position on the chromosome for the regions to query.
- end : integer vector, ending position on the chromosome for the regions to query.
- value : single character value, name of the column to use for state assignation.
- na : single character value, see penetrance() help page for details ('false' is not handled).
- fuzzy : single logical value, whether to assign the state when some sub-regions are out or not.
- states : list of states, see penetrance help page for details.

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.array-class, process, tk.process, refTable-class

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