BiasBoss Class Reference

The BiasBoss class keeps track of sequence-specific and positional bias. More...

#include <biascorrection.h>

List of all members.

Public Member Functions
	BiasBoss (size_t order, double alpha)
	BiasBoss Constructor.
	BiasBoss (size_t order, std::string param_file_name)
	A second constructor that loads the distributions from a parameter file.
size_t	order () const
	An accessor for the order of the Markov chains used to model the sequences.
void	copy_observations (const BiasBoss &other)
	A member function that copies the observed parameters from another BiasBoss.
void	copy_expectations (const BiasBoss &other)
	A member function that copies the expected parameters from another BiasBoss.
void	update_expectations (const Target &targ, double mass=0, const std::vector< double > &fl_cdf=std::vector< double >())
	A member function that updates the expectation parameters assuming uniform abundance of and coverage accross the target's sequence.
void	normalize_expectations ()
	A member function that normalizes the expected counts and fills in the lower-ordered marginals.
void	update_observed (const FragHit &hit, double mass)
	A member function that updates the observed parameters given a fragment mapping to a target and its logged probabilistic assignment value.
double	get_target_bias (std::vector< float > &start_bias, std::vector< float > &end_bias, const Target &targ) const
	A member function that returns the 5' and 3' bias values at each position in a given target based on the current bias parameters.
void	append_output (std::ofstream &outfile) const
	A member function that appends the 5' and 3' bias parameters to the given file, formatted in tables for easy readability.

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Detailed Description

The BiasBoss class keeps track of sequence-specific and positional bias.

It allows for the bias associated with a given fragment end to be calculated, and

for the bias parameters to be updated based on additional observations. All stored and returned values are in log space.

Author:

Adam Roberts

Date:

2011 Artistic License 2.0

Definition at line 138 of file biascorrection.h.

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Constructor & Destructor Documentation

BiasBoss::BiasBoss	(	size_t	order,
		double	alpha
	)

BiasBoss Constructor.

Parameters:

order	a size_t specifying the order of the Markov chains used to model the sequences.
alpha	a double specifying the strength of the uniform prior (logged pseudo-counts for each parameter).

Definition at line 185 of file biascorrection.cpp.

BiasBoss::BiasBoss	(	size_t	order,
		std::string	param_file_name
	)

A second constructor that loads the distributions from a parameter file.

Note that the values should not be modified after using this constructor.

Parameters:

order	a size_t specifying the order to use for the Markov chains modelling the sequence. Must match file.
param_file_name	a string specifying the path to the parameter file.

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Member Function Documentation

void BiasBoss::append_output

(

std::ofstream &

outfile

)

const

A member function that appends the 5' and 3' bias parameters to the given file, formatted in tables for easy readability.

Parameters:

outfile

the file to append to.

void BiasBoss::copy_expectations

(

const BiasBoss &

other

)

A member function that copies the expected parameters from another BiasBoss.

Parameters:

other

a BiasBoss to copy the parameters from.

Definition at line 202 of file biascorrection.cpp.

void BiasBoss::copy_observations

(

const BiasBoss &

other

)

A member function that copies the observed parameters from another BiasBoss.

Parameters:

other

a BiasBoss to copy the parameters from.

Definition at line 197 of file biascorrection.cpp.

double BiasBoss::get_target_bias	(	std::vector< float > &	start_bias,
		std::vector< float > &	end_bias,
		const Target &	targ
	)		const

A member function that returns the 5' and 3' bias values at each position in a given target based on the current bias parameters.

Parameters:

start_bias	a vector containing the logged bias for each 5' start site in the target.
end_bias	a vector containing the logged bias for each 3' end site in the target.
targ	the target for which to calculate the bias.

Returns:

The product of the average 5' and 3' bias (logged).

Definition at line 244 of file biascorrection.cpp.

size_t BiasBoss::order

(

)

const [inline]

An accessor for the order of the Markov chains used to model the sequences.

Returns:

The order of the Markov chains used to model the sequences.

Definition at line 177 of file biascorrection.h.

void BiasBoss::update_expectations	(	const Target &	targ,
		double	mass = 0,
		const std::vector< double > &	fl_cdf = std::vector<double>()
	)

A member function that updates the expectation parameters assuming uniform abundance of and coverage accross the target's sequence.

Parameters:

targ	the target to measure expected counts from

Definition at line 207 of file biascorrection.cpp.

void BiasBoss::update_observed	(	const FragHit &	hit,
		double	mass
	)

A member function that updates the observed parameters given a fragment mapping to a target and its logged probabilistic assignment value.

Parameters:

hit	the fragment hit (alignment).
mass	the logged probabality of the mapping, which is the amount to increment the observed counts by.

Definition at line 228 of file biascorrection.cpp.

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The documentation for this class was generated from the following files:

• src/biascorrection.h
• src/biascorrection.cpp