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Class CGH

The class CGH describes a single aberation in CGH (Comparative Genome Hybridisation) notation. Such an aberration is described by its location on a chromosome and the type of aberration (enh, amp, dim). The start and end bands of the fragment with changed quantity are not regarded as break points.

CGH

New()

New(ByRef Fragment: Fragment, CGHType: CGHTypes)

clone(): Object

compareTo(obj: Object): Integer

getCGHType(): CGHTypes

getFragment(): Fragment

getQuantitativeAberration(): QuantitativeAberration

toString(): String

Programming Language

Microsoft Visual Basic .Net.

Availability

Copyrighted but free software under the GNU Public License.
Binaries and source code can be obtained from the Download section.

Constructors

Public Sub New

This parameter-less constructor is needed for cloning purposes and must be public because of COM compatibility. It is not intended for normal use. DO NOT USE IT.

Public Sub New(ByRef Fragment As Fragment, ByVal CGHType As CGHTypes)

Instantiates a new CGH object.

Parameters

Fragment: a reference to the Fragment object describing the chromosomal region affected by this aberration.
CGHType: the type of the aberration. Acceptable Values are defined in the CGHTypes enumeration.

Exceptions

ArgumentOutOfRangeException: If the start band or the end band of the fragment are not defined in the resources, an ArgumentOutOfRangeException containing a description of the problem is thrown.

Remarks

Normally, a CGH object will be instantiated from the constructor of the CGHs object.
Bands are checked with the ChromosomeData.checkBandExistence function.

Interfaces

IComparable

is implemented with the compareTo function.

ICloneable

is implemented with the clone function.

Enumerations

The class provides an enumeration for types of an aberration defined for CGH.

Enum CGHTypes

This enumeration describes the the type of aberration.

Value	Meaning
CGH_Dim (= 1)	the signal for the fragment is "diminished".
CGH_Enh (= 2)	the signal for the fragment is "enhanced".
CGH_Amp (= 0)	the signal for the fragment is "amplified".

Properties

Since the CGH object expects not to be changed after its initialisation, all its properties are read-only. They were made available through their respective getPropertyName functions only (see below).

Methods

Public Function clone() As Object Implements ICloneable.Clone

Returns a copy of the CGH object.

Return Value

A copy of the CGH object.

Implements

ICloneable.Clone

Remarks

The Fragment object contained in the CGH object is also cloned.

Public Function compareTo(ByVal obj As Object) As Integer Implements IComparable.CompareTo

Compares this instance to a specified CGH object and returns an indication of their relative values.

Return Value

<0: This object has a lower type of aberration, or if the objects share the aberration type, the fragment of this chromosome comes before the fragment of obj.
0: The CGH obejcts are equal.
>0: This object has a higher type of aberration, or if the objects share the aberration type, the fragment of this chromosome comes after the fragment of obj.

Parameters

obj: the CGH object to be compared with this CGH object.

Exceptions

ArgumentException: is thrown when obj cannot be cast into CGH type.

Implements

IComparable.CompareTo

Remarks

In a first step, CGH objects are compared by their aberration types, with their symbols being ordered alphabetically.
If the objects share the aberration type, the start bands of the fragments are compared, and if they are equal in turn, their end bands are compared using Band.compareTo(obj).
The sorting order of chromosome follows the specification given in "ISCN 1995" by F. Mitelman et al. Bands on the same chromosome are sorted along the plus strand, i.e. from p terminus to q terminus.

Public Function getCGHType() As CGHTypes

Gets the type of aberration associated with this CGH object.

Property Value

the type of aberration.

Remarks

The values for the CGHType are defined in the CGHTypes enumeration.

Public Function getFragment() As Fragment

Gets the fragment associated with this aberration.

Public Function getQuantitativeAberration() As QuantitativeAberration

Returns the QuantitativeAberration implied by this aberration.

Return Value

the QuantitativeAberration implied by this aberration.

Remarks

"amp" is translated into a gain fo the fragment, the multiplicators of the QuantitativeAberration being 2.
"enh" is translated into a gain fo the fragment, the multiplicators of the QuantitativeAberration being 1.
"dim" is translated into a loss fo the fragment, the multiplicators of the QuantitativeAberration being 1.

Examples

"amp(2q21q23)" corresponds to "+(2)(q21q23)x2" in SCCN.
"enh(2q21q23)" corresponds to "+(2)(q21q23)" in SCCN.
"dim(2q21q23)" corresponds to "-(2)(q21q23)" in SCCN.

Public Function toString() As String

Returns a textual description of this CGH element using the CGH-typical nomenclature.

Return Value

a textual description of this CGH element.

Remarks

For output of the fragment, Fragment.toString("C") is called.

Examples

An amplified fragment from 2q21 to 2q23 is translated to "amp(2q21q23)".
An enhanced fragment from 2q21 to 2q23 is translated to "enh(2q21q23)".
A diminished fragment from 2q21 to 2q23 is translated to "dim(2q21q23)".

Interaction with other classes

Classes using CGH

The CGH class is integral part of its collection class CGHs.

Classes used by CGH

The CGH class uses a Fragment object to store the fragment affected by the aberration. The ChromosomeData class is used for checking the existence of the bands of the fragment. A QuantitativeAberration object is calculated transiently in the getQuantitativeAberration function.