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.
Overview
Programming Language
-
Microsoft Visual Basic .Net.
Availability
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
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 get
PropertyName 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
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
Implements
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
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
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
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.
