CpGIslandFinder
in package
implements
CpGIslandFinderInterface
Net-new (present in neither BioPHP nor biotools). Implements the classic Gardiner-Garden & Frommer (1987) criteria : a window qualifies when its GC content and its observed/expected CpG ratio - Obs/Exp = (CpG count * window length) / (C count * G count), the standard formula - both clear their threshold. Every scanned window is independent ; consecutive or overlapping qualifying windows are then merged into a single island, whose own gcContent/observedToExpectedRatio are recomputed over its full merged span rather than inherited from whichever window first qualified, so they describe the island actually reported. Reuses SkewCalculator for the GC content half of the criteria rather than re-counting bases a second time.
Class CpGIslandFinder
Tags
Table of Contents
Interfaces
- CpGIslandFinderInterface
- Interface CpGIslandFinderInterface - finds CpG islands using the classic Gardiner-Garden & Frommer (1987) criteria : GC content and observed/expected CpG ratio both above a threshold, over a sliding window.
Properties
Methods
- __construct() : mixed
- CpGIslandFinder constructor.
- findIslands() : array<string|int, CpGIsland>
- observedToExpectedRatio() : float
- qualifies() : bool
Properties
$skewCalculator
private
SkewCalculatorInterface
$skewCalculator
Methods
__construct()
CpGIslandFinder constructor.
public
__construct(SkewCalculatorInterface $oSkewCalculator) : mixed
Parameters
- $oSkewCalculator : SkewCalculatorInterface
findIslands()
public
findIslands(DnaSequence $oSequence[, int $iWindowSize = 200 ][, int $iStep = 1 ][, float $fMinGcContent = 0.5 ][, float $fMinObservedToExpectedRatio = 0.6 ]) : array<string|int, CpGIsland>
Parameters
- $oSequence : DnaSequence
- $iWindowSize : int = 200
- $iStep : int = 1
- $fMinGcContent : float = 0.5
- $fMinObservedToExpectedRatio : float = 0.6
Return values
array<string|int, CpGIsland>observedToExpectedRatio()
private
observedToExpectedRatio(string $sSequence) : float
Parameters
- $sSequence : string
Return values
float —0.0 when the sequence has no C or no G at all
qualifies()
private
qualifies(string $sWindow, float $fMinGcContent, float $fMinObservedToExpectedRatio) : bool
Parameters
- $sWindow : string
- $fMinGcContent : float
- $fMinObservedToExpectedRatio : float