fextract_relative_entropy_to_flanking package

Submodules

fextract_relative_entropy_to_flanking.plugin module

class lbfextract.fextract_relative_entropy_to_flanking.plugin.CliHook[source]

Bases: object

This CliHook implements the CLI interface for the extract_relative_entropy_to_flanking feature extraction method.

extract_relative_entropy_to_flanking

Given a set of genomic intervals having the same length w, extract_relative_entropy_to_flanking calculates the Relative Fragment Entropy at each position, which can be represented as:

\[RFE_l = D_{KL}(Q_l | F) = \sum_{x \in X} Q_l(x) log(\frac{Q_l(x)}{F(x)})\]

Where \(l\) represents the genomic position, \(Q_l\) represents the fragment length distribution at position \(l\), \(X\) is the alphabet (fragment length range used) and \(F\) is the fragment length distribution in the flanking region

get_command() → Command | List[Command][source]
class lbfextract.fextract_relative_entropy_to_flanking.plugin.FextractHooks[source]

Bases: object

plot_signal(signal: Signal, config: Any, extra_config: AppExtraConfig) → Figure[source]
transform_all_intervals(single_intervals_transformed_reads: Signal, config: Any, extra_config: Any) → Signal[source]
Parameters:

  • single_intervals_transformed_reads – Signal object containing the signals per interval

  • config – config specific to the function

  • extra_config – extra configuration that may be used in the hook implementation

Module contents