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

In cghRA: Array CGH Data Analysis and Visualization

Description

This class is the main component of the cghRA object-oriented package. Each CGH array must be stored in a distinct cghRA.array object.

Objects from this class should always be produced by the cghRA.array constructor.

This class is a hub, it provides methods to apply various CGH analysis tools in a straight-forward way.

The Reference Class system is used notably to share designs objects between arrays, as several arrays may have values for the same probes.

Extends

Class crossable, directly.
Class sliceable, by class crossable, distance 2.
Class drawable, by class crossable, distance 3.

All reference classes extend and inherit methods from envRefClass.

Fields

assembly:

Single character value, the assembly version for the coordinates stored in the object. Must have length 1, should not be NA.

design:

Object of class cghRA.design

organism:

Single character value, the name of the organism whose data is stored in the object. Must have length 1, should not be NA.

probes:

Object of class cghRA.probes.

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

• name (drawable)

• parameters (drawable)

Methods

as.CNA():

Returns a CNA object (DNAcopy) with the object content.

as.profileCGH(chrom = , quiet = ):

Returns a profileCGH object (GLAD) with the object content.
- chrom : single character value defining how to deal with chromosome names :
'merged' forces chromosome arms to be merged (as chromosome arms are not handled)
'levels' converts chromosome to integers (can be deceiving for factors)
- quiet : single logical value, whether to warn for factor to integer conversion or not.

DLRS(method = , na.rm = ):

Computes the Derivative Log Ratio Spread from the probes.
- method : 'agilent' or 'original', implying distinct formulas.

DNAcopy(smooth = , ...):

Apply the Circular Binary Segmentation, as implemented in DNAcopy, and return a cghRA.regions object.
- smooth : a list of arguments to be passed to smooth.CNA(), TRUE to use the default parameters or FALSE to skip smoothing.
- ... : arguments to be passed to segment().

extract(i = , j = ):

Extracts values from 'probes' and 'design' into a data.frame.
- i : row selection, see the R5Table method for further details.
- j : column selection, see the R5Table method for further details.

GADA(...):

Apply the Genome Alteration Detection Analysis, as implemented in GADA, and return a cghRA.regions object.
- smooth : a list of arguments to be passed to smooth.CNA(), TRUE to use the default parameters or FALSE to skip smoothing.
- ... : arguments to be passed to segment().

GLAD(chrom = , quiet = , output = , ...):

Apply the Gain and Loss Analysis of Dna, as implemented in GLAD, and return a cghRA.regions object.
- chrom, quiet : to be passed to the as.profileCGH method.
- output : single character value defining the returned value :
'regions' returns a cghRA.regions object with the segmented genome
'raw' returns the glad() output
'both' adds a 'cghRA.regions' element to the glad() output list to return both
- ... : arguments to be passed to glad().

MAplot(pch = , cex = , xlab = , ylab = , ...):

MA plot of all the probes.
- ... : arguments to be passed to plot().

maskByFlag(flags = , pattern = , multiple = , na = ):

Replaces logRatios of flagged probes by NA.
- flags : character vector, the columns to coerce as boolean and use as flags.
- pattern : single logical value, whether to consider 'flags' as regular expressions or fixed values.
- multiple : mask a probe when 'all' its flag columns are TRUE or when 'any' is.

replicates(fun = , na.rm = , ...):

Apply 'fun' to replicated probes (same name), masking all members but one.
- fun : single character value, the function to apply.
- ... : to be passed to 'fun'.

spatial(filename = , palSize = , palEnds = , ...):

Produces a spatial representation of the logRatios, to identify spatial biases.
- filename : single character value, the path to the PNG output.
- palSize : single integer value, the amount of color levels for logRatios. Should be lesser or equal to 254 to produce small PNG files.
- palEnds : character vector to be passed to colorRampPalette() for palette generation.

WACA():

Apply the Waves aCGH Correction Algorithm (Lepretre et al. 2009) to the array logRatios.

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

• callParams (drawable)

• callSuper (envRefClass)

• check (drawable, overloaded)

• chromosomes (drawable, overloaded)

• copy (envRefClass)

• cross (crossable)

• defaultParams (sliceable, overloaded)

• draw (sliceable)

• export (envRefClass)

• field (envRefClass)

• fix.param (drawable)

• getChromEnd (sliceable, overloaded)

• getClass (envRefClass)

• getName (drawable)

• getParam (drawable)

• getRefClass (envRefClass)

• import (envRefClass)

• initFields (envRefClass)

• initialize (drawable, overloaded)

• setName (drawable)

• setParam (drawable)

• show (sliceable, overloaded)

• slice (sliceable, overloaded)

• trace (envRefClass)

• untrace (envRefClass)

• usingMethods (envRefClass)

Author(s)

Sylvain Mareschal

See Also

cghRA.array

cghRA.series-class, cghRA.design-class, cghRA.probes-class, cghRA.regions-class

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