Package Bio :: Package Motif :: Module Thresholds :: Class ScoreDistribution

Class ScoreDistribution

object --+
         |
        ScoreDistribution

Class representing approximate score distribution for a given motif.

Utilizes a dynamic programming approch to calculate the distribution of scores with a predefined precision. Provides a number of methods for calculating thresholds for motif occurences.

Instance Methods

[hide private]

__init__(self, motif, precision=1000)
x.__init__(...) initializes x; see help(type(x)) for signature

source code

_index_diff(self, x, y=0.0)

source code

_add(self, i, j)

source code

modify(self, scores, mo_probs, bg_probs)

source code

threshold_fpr(self, fpr)
Approximate the log-odds threshold which makes the type I error (false positive rate).

source code

threshold_fnr(self, fnr)
Approximate the log-odds threshold which makes the type II error (false negative rate).

source code

threshold_balanced(self, rate_proportion=1.0, return_rate=False)
Approximate the log-odds threshold which makes FNR equal to FPR times rate_proportion

source code

threshold_patser(self)
Threshold selection mimicking the behaviour of patser (Hertz, Stormo 1999) software.

source code

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

Properties

[hide private]

Inherited from object: __class__

Method Details

[hide private]

init(self, motif, precision=1000)
(Constructor)

source code

x.__init__(...) initializes x; see help(type(x)) for signature

Overrides: object.__init__: (inherited documentation)

threshold_patser(self)

source code

Threshold selection mimicking the behaviour of patser (Hertz, Stormo 1999) software.

It selects such a threshold that the log(fpr)=-ic(M) note: the actual patser software uses natural logarithms instead of log_2, so the numbers are not directly comparable.

Class ScoreDistribution

__init__(self, motif, precision=1000) (Constructor)

threshold_patser(self)

init(self, motif, precision=1000)
(Constructor)