#include <ms_imputation.hpp>

Inheritance diagram for ms_imputation:

Collaboration diagram for ms_imputation:

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Public Types
enum	IMPUTATION_VARIABLE { IMPUTE_PROTEIN_RATIO , IMPUTE_PEPTIDE_RATIO , IMPUTE_RETENTION_TIME }
	What type of data is being imputed. More...

Public Member Functions
	ms_imputation (const ms_ms1quantitation *ms1quantitation, ms_imputation_method &m, IMPUTATION_VARIABLE imputationVariableChoice)
	Use this contructor to create an object to impute missing ms1 ratio values.

	ms_imputation (const ms_ms2quantitation *ms2quantitation, ms_imputation_method &m, IMPUTATION_VARIABLE imputationVariableChoice)
	Use this contructor to create an object to impute missing ms2 ratio values.

	~ms_imputation ()
	Imputation Destructor.

void	appendErrors (const ms_errors &src)
	Copies all errors from another instance and appends them at the end of own list.

void	clearAllErrors ()
	Remove all errors from the current list of errors.

void	copyFrom (const ms_errors *right)
	Use this member to make a copy of another instance.

const ms_errs *	getErrorHandler () const
	Retrive the error object using this function to get access to all errors and error parameters.

const IMPUTATION_VARIABLE	getImputationVariableChoice () const
	Get what the imputation object is currently imputing. I.e. protein/peptide ratios from ms1 or ms2 quantitation, or retention times for label free quantitation.

bool	getImputeExcludedMs2PeptideRatios ()
	Get how the imputation object is currently treating ms2 excluded ratios. I.e. are excluded ratios treated as missing. Not used when imputing ms1 quantitation results.

bool	getImputeMs1PeptideExcludedByCorrelationThr ()
	Get how the imputation object is currently treating ms1 peptide ratios excluded because of the fraction threshold. Not used when imputing ms2 quantitation results.

bool	getImputeMs1PeptideExcludedByFractionThr ()
	Get how the imputation object is currently treating ms1 peptide ratios excluded because of the fraction threshold. Not used when imputing ms2 quantitation results.

bool	getImputeMs1PeptideExcludedByStdErrThr ()
	Get how the imputation object is currently treating ms1 peptide ratios excluded because of the std err threshold. Not used when imputing ms2 quantitation results.

bool	getImputeMs1PeptideNegativeRatio ()
	Get how the imputation object is currently treating negative ms1 peptide ratios. Not used when imputing ms2 quantitation results.

int	getLastError () const
	Return the error description of the last error that occurred.

std::string	getLastErrorString () const
	Return the error description of the last error that occurred.

std::vector< std::vector< double > >	impute ()
	Returns a 2D (m,n) array of doubles. m is the number of variables, implemented so far is quantitation ratios or subprojects n is the number of observations, implemented so far is the number of protein or peptides.

bool	isValid () const
	Call this function to determine if there have been any errors.

void	setImputationVariableChoice (const IMPUTATION_VARIABLE imputationVariableChoiceIn)
	Set the imputation object to impute protein/peptide ratios from ms1 or ms2 quantitation, or retention times for label free quantitation.

void	setImputeExcludedMs2PeptideRatios (bool imputationMs2PeptideChoiceIn)
	Set the imputation object to treat excluded ms2 ratios as missing Not used when imputing ms1 quantitation results.

void	setImputeMs1PeptideExcludedByCorrelationThr (bool imputeMs1PeptideExcludedByCorrelationThr)
	Set the imputation object behaviour of ms1 peptide ratios excluded because of the fraction threshold. Not used when imputing ms2 quantitation results.

void	setImputeMs1PeptideExcludedByFractionThr (bool imputeMs1PeptideExcludedByFractionThr)
	Set the imputation object behaviour of ms1 peptide ratios excluded because of the fraction threshold. Not used when imputing ms2 quantitation results.

void	setImputeMs1PeptideExcludedByStdErrThr (bool imputeMs1PeptideExcludedByStdErrThr)
	Set the imputation object behaviour of ms1 peptide ratios excluded because of the std err threshold. Not used when imputing ms2 quantitation results.

void	setImputeMs1PeptideNegativeRatio (bool imputeMs1PeptideNegativeRatio)
	Set the imputation object behaviour of negative ms1 peptide ratios. Not used when imputing ms2 quantitation results.

Detailed Description

This class is the main conduit to execute numerical methods used to predict or impute missing values within incomplete arrays of data.

EXPERIMENTAL: This class is EXPERIMENTAL. Both the API and the implementation may change in a future version of Parser.

Data is set using the supplied quantitation objects on ratio or retention time values.

Member Enumeration Documentation

◆ IMPUTATION_VARIABLE

enum IMPUTATION_VARIABLE

What type of data is being imputed.

Use in the ms1 and ms2 ms_imputation constructors to declare the choice of ratios being imputed.

See Using enumerated values and static const ints in Perl, Java, Python and C#.

Enumerator
IMPUTE_PROTEIN_RATIO	Missing protein ratios are imputed.
IMPUTE_PEPTIDE_RATIO	Missing peptide ratios are imputed. How to treat excluded peptide ratios is set via setImputeMs1PeptideExcludedByFractionThr and similarly named get/setters or by setImputeExcludedMs2PeptideRatios.
IMPUTE_RETENTION_TIME	Missing peptide retention times are being imputed.

Constructor & Destructor Documentation

◆ ms_imputation() [1/2]

ms_imputation	(	const ms_ms1quantitation *	ms1quantitation,
		ms_imputation_method &	m,
		IMPUTATION_VARIABLE	imputationVariableChoice
	)

Use this contructor to create an object to impute missing ms1 ratio values.

Use this constructor for when imputing missing ratio values from ms1 quantitation.

Parameters

ms1quantitation	is a pointer to the ms1 quantitation object.
m	is a reference to the chosen imputation method object.
imputationVariableChoice	is an enum of which values to impute. Only protein or peptide.

◆ ms_imputation() [2/2]

ms_imputation	(	const ms_ms2quantitation *	ms2quantitation,
		ms_imputation_method &	m,
		IMPUTATION_VARIABLE	imputationVariableChoice
	)

Use this contructor to create an object to impute missing ms2 ratio values.

Use this constructor for when imputing missing ratio values from ms2 quantitation.

Parameters

ms2quantitation	is a pointer to the ms2 quantitation object.
m	is a reference to the chosen imputation method object.
imputationVariableChoice	is an enum of which values to impute. Only protein or peptide.

Member Function Documentation

◆ appendErrors()

void appendErrors ( const ms_errors & src )

inherited

Copies all errors from another instance and appends them at the end of own list.

Parameters

src	The object to copy the errors across from. See Maintaining object references: two rules of thumb.

◆ clearAllErrors()

void clearAllErrors ( )

inherited

Remove all errors from the current list of errors.

The list of 'errors' can include fatal errors, warning messages, information messages and different levels of debugging messages.

All messages are accumulated into a list in this object, until clearAllErrors() is called.

See Error Handling.

See also: isValid(), getLastError(), getLastErrorString(), getErrorHandler()

Examples: common_error.cpp, resfile_error.cpp, and resfile_summary.cpp.

◆ copyFrom()

void copyFrom ( const ms_errors * right )

inherited

Use this member to make a copy of another instance.

Parameters

right is the source to initialise from

◆ getErrorHandler()

const ms_errs * getErrorHandler ( ) const

inherited

Retrive the error object using this function to get access to all errors and error parameters.

See Error Handling.

Returns: Constant pointer to the error handler

See also: isValid(), getLastError(), getLastErrorString(), clearAllErrors(), getErrorHandler()

Examples: common_error.cpp, and http_helper_getstring.cpp.

◆ getLastError()

int getLastError ( ) const

inherited

Return the error description of the last error that occurred.

All errors are accumulated into a list in this object, until clearAllErrors() is called. This function returns the last error that occurred.

See Error Handling.

See also: isValid(), getLastErrorString(), clearAllErrors(), getErrorHandler()

Returns: the error number of the last error, or 0 if there have been no errors.

◆ getLastErrorString()

std::string getLastErrorString ( ) const

inherited

Return the error description of the last error that occurred.

All errors are accumulated into a list in this object, until clearAllErrors() is called. This function returns the last error that occurred.

Returns: Most recent error, warning, information or debug message

See Error Handling.

See also: isValid(), getLastError(), clearAllErrors(), getErrorHandler()

Examples: common_error.cpp, config_enzymes.cpp, config_fragrules.cpp, config_license.cpp, config_mascotdat.cpp, config_masses.cpp, config_modfile.cpp, config_procs.cpp, config_quantitation.cpp, config_taxonomy.cpp, http_helper_getstring.cpp, and tools_aahelper.cpp.

◆ impute()

std::vector< std::vector< double > > impute ( )

Returns a 2D (m,n) array of doubles. m is the number of variables, implemented so far is quantitation ratios or subprojects n is the number of observations, implemented so far is the number of protein or peptides.

The 2D array will contain a mixture of real double values and imputed double values where previously there was missing values. The imputation method executed will be the type chosen in the ms_imputation constructor.

Returns: The 2D array of double values.

◆ isValid()

bool isValid ( ) const

inherited

Call this function to determine if there have been any errors.

This will return true unless there have been any fatal errors.

See Error Handling.

Returns: True if no fatal error occured

See also: getLastError(), getLastErrorString(), clearAllErrors(), getErrorHandler()

Examples: common_error.cpp, config_enzymes.cpp, config_fragrules.cpp, config_license.cpp, config_mascotdat.cpp, config_masses.cpp, config_modfile.cpp, config_procs.cpp, config_quantitation.cpp, config_taxonomy.cpp, http_helper_getstring.cpp, peptide_list.cpp, repeat_search.cpp, resfile_error.cpp, resfile_info.cpp, resfile_input.cpp, resfile_params.cpp, resfile_summary.cpp, and tools_aahelper.cpp.

◆ setImputeMs1PeptideExcludedByCorrelationThr()

void setImputeMs1PeptideExcludedByCorrelationThr ( bool imputeMs1PeptideExcludedByCorrelationThr )

Set the imputation object behaviour of ms1 peptide ratios excluded because of the fraction threshold. Not used when imputing ms2 quantitation results.

Set how the imputation object is currently treating ms1 peptide ratios excluded because of the std err threshold.

Parameters

imputeMs1PeptideExcludedByCorrelationThr is a bool to set if ms1 peptide ratio values excluded by fraction threshold are treated as missing values or not.

◆ setImputeMs1PeptideExcludedByFractionThr()

void setImputeMs1PeptideExcludedByFractionThr ( bool imputeMs1PeptideExcludedByFractionThr )

Set the imputation object behaviour of ms1 peptide ratios excluded because of the fraction threshold. Not used when imputing ms2 quantitation results.

Set how the imputation object is currently treating ms1 peptide ratios excluded because of the fraction threshold.

Parameters

imputeMs1PeptideExcludedByFractionThr is a bool to set if ms1 peptide ratio values excluded by fraction threshold are treated as missing values or not.

◆ setImputeMs1PeptideExcludedByStdErrThr()

void setImputeMs1PeptideExcludedByStdErrThr ( bool imputeMs1PeptideExcludedByStdErrThr )

Set the imputation object behaviour of ms1 peptide ratios excluded because of the std err threshold. Not used when imputing ms2 quantitation results.

Set how the imputation object is currently treating ms1 peptide ratios excluded because of the std err threshold.

Parameters

imputeMs1PeptideExcludedByStdErrThr is a bool to set if ms1 peptide ratio values excluded by std err threshold are treated as missing values or not.

◆ setImputeMs1PeptideNegativeRatio()

void setImputeMs1PeptideNegativeRatio ( bool imputeMs1PeptideNegativeRatio )

Set the imputation object behaviour of negative ms1 peptide ratios. Not used when imputing ms2 quantitation results.

Set how the imputation object is currently treating ms1 peptide ratios excluded because of the std err threshold.

Parameters

imputeMs1PeptideNegativeRatio is a bool to set if negative ms1 peptide ratio values are treated as missing values or not.

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

ms_imputation.hpp
ms_imputation.cpp

Public Types

Public Member Functions

Detailed Description

Member Enumeration Documentation

◆ IMPUTATION_VARIABLE

Constructor & Destructor Documentation

◆ ms_imputation() [1/2]

◆ ms_imputation() [2/2]

Member Function Documentation

◆ appendErrors()

◆ clearAllErrors()

◆ copyFrom()

◆ getErrorHandler()

◆ getLastError()

◆ getLastErrorString()

◆ impute()

◆ isValid()

◆ setImputeMs1PeptideExcludedByCorrelationThr()

◆ setImputeMs1PeptideExcludedByFractionThr()

◆ setImputeMs1PeptideExcludedByStdErrThr()

◆ setImputeMs1PeptideNegativeRatio()