SkewResult
in package
A skew with an undefined denominator (e.g. GC-skew over a window with no G or C at all) is 0.0 rather than thrown or NAN - a deliberate, documented choice (SkewCalculator's own docblock) so a sliding window never has to special-case an all-A/T or otherwise degenerate window.
Class SkewResult
Tags
Table of Contents
Properties
- $atSkew : float
- $gcContent : float
- $gcSkew : float
- $ketoSkew : float
Methods
- __construct() : mixed
- SkewResult constructor.
- getAtSkew() : float
- 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
- getGcSkew() : float
- getKetoSkew() : float
Properties
$atSkew
private
float
$atSkew
(A-T)/(A+T) ; 0.0 when A+T=0
$gcContent
private
float
$gcContent
AbstractNucleicSequence::gcFraction() : (G+C+S)/(A+C+G+T+S+W) ; 0.0 for a window with none of these bases
$gcSkew
private
float
$gcSkew
(G-C)/(G+C) ; 0.0 when G+C=0
$ketoSkew
private
float
$ketoSkew
(G+T-A-C)/(A+C+G+T), keto (K) minus amino (M) bases ; 0.0 for an empty window
Methods
__construct()
SkewResult constructor.
public
__construct(float $fGcSkew, float $fAtSkew, float $fKetoSkew, float $fGcContent) : mixed
Parameters
- $fGcSkew : float
- $fAtSkew : float
- $fKetoSkew : float
- $fGcContent : float
getAtSkew()
public
getAtSkew() : float
Return values
floatgetGcContent()
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
getGcSkew()
public
getGcSkew() : float
Return values
floatgetKetoSkew()
public
getKetoSkew() : float