CpGIsland
in package
FinalYes
Coordinates are 1-based inclusive, the convention the rest of this project uses. gcContent and observedToExpectedRatio are computed over the island's own full span - once it is known, not inherited from whichever single scanning window first triggered its detection - so they describe the island actually reported, not an arbitrary window inside it.
Class CpGIsland
Tags
Table of Contents
Properties
- $end : int
- $gcContent : float
- $observedToExpectedRatio : float
- $start : int
Methods
- __construct() : mixed
- CpGIsland constructor.
- getEnd() : int
- getGcContent() : float
- The G+C content as a FRACTION, 0 to 1 - not the percentage AbstractNucleicSequence::getGcContent() gives under the same name. Kept as it is ; getGcFraction() and getGcPercent() say their scale.
- getGcFraction() : float
- getGcPercent() : float
- getLength() : int
- getObservedToExpectedRatio() : float
- getStart() : int
Properties
$end
private
int
$end
1-based inclusive
$gcContent
private
float
$gcContent
$observedToExpectedRatio
private
float
$observedToExpectedRatio
$start
private
int
$start
1-based inclusive
Methods
__construct()
CpGIsland constructor.
public
__construct(int $iStart, int $iEnd, float $fGcContent, float $fObservedToExpectedRatio) : mixed
Parameters
- $iStart : int
- $iEnd : int
- $fGcContent : float
- $fObservedToExpectedRatio : float
getEnd()
public
getEnd() : int
Return values
intgetGcContent()
The G+C content as a FRACTION, 0 to 1 - not the percentage AbstractNucleicSequence::getGcContent() gives under the same name. Kept as it is ; getGcFraction() and getGcPercent() say their scale.
public
getGcContent() : float
Return values
floatgetGcFraction()
public
getGcFraction() : float
Return values
float —The G+C content as a fraction, 0 to 1
getGcPercent()
public
getGcPercent() : float
Return values
float —The G+C content as a percentage, 0 to 100
getLength()
public
getLength() : int
Return values
intgetObservedToExpectedRatio()
public
getObservedToExpectedRatio() : float
Return values
floatgetStart()
public
getStart() : int