CpGIslandFinderInterface
in
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.
Tags
Table of Contents
Methods
- findIslands() : array<string|int, CpGIsland>
Methods
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
-
0.5 = 50%, the usual Gardiner-Garden & Frommer threshold
- $fMinObservedToExpectedRatio : float = 0.6
-
0.6, the usual threshold
Return values
array<string|int, CpGIsland> —In ascending order of start position, never overlapping