This class holds the functionality of calculating the database suitability. More...

#include <OpenMS/QC/DBSuitability.h>

Inheritance diagram for DBSuitability:

Collaboration diagram for DBSuitability:

Classes
struct	SuitabilityData
	struct to store results More...

Public Member Functions
	DBSuitability ()

	~DBSuitability ()=default
	Destructor. More...

void	compute (std::vector< PeptideIdentification > pep_ids)
	Computes suitability of a database used to search a mzML. More...

const std::vector< SuitabilityData > &	getResults () const
	Returns results calculated by this metric. More...

Public Member Functions inherited from DefaultParamHandler
	DefaultParamHandler (const String &name)
	Constructor with name that is displayed in error messages. More...

	DefaultParamHandler (const DefaultParamHandler &rhs)
	Copy constructor. More...

virtual	~DefaultParamHandler ()
	Destructor. More...

virtual DefaultParamHandler &	operator= (const DefaultParamHandler &rhs)
	Assignment operator. More...

virtual bool	operator== (const DefaultParamHandler &rhs) const
	Equality operator. More...

void	setParameters (const Param &param)
	Sets the parameters. More...

const Param &	getParameters () const
	Non-mutable access to the parameters. More...

const Param &	getDefaults () const
	Non-mutable access to the default parameters. More...

const String &	getName () const
	Non-mutable access to the name. More...

void	setName (const String &name)
	Mutable access to the name. More...

const std::vector< String > &	getSubsections () const
	Non-mutable access to the registered subsections. More...

Private Member Functions
double	getDecoyDiff_ (const PeptideIdentification &pep_id)
	Calculates the xcorr difference between the top two hits marked as decoy. More...

double	getDecoyCutOff_ (const std::vector< PeptideIdentification > &pep_ids, double reranking_cutoff_percentile)
	Calculates a xcorr cut-off based on decoy hits. More...

bool	isNovoHit_ (const PeptideHit &hit)
	Tests if a PeptideHit is considered a deNovo hit. More...

bool	passesFDR_ (const PeptideHit &hit, double FDR)
	Tests if a PeptideHit has a lower q-value than the given FDR threshold, i.e. passes FDR. More...

Private Attributes
std::vector< SuitabilityData >	results_
	result vector More...

Additional Inherited Members
Static Public Member Functions inherited from DefaultParamHandler
static void	writeParametersToMetaValues (const Param &write_this, MetaInfoInterface &write_here, const String &prefix="")
	Writes all parameters to meta values. More...

Protected Member Functions inherited from DefaultParamHandler
virtual void	updateMembers_ ()
	This method is used to update extra member variables at the end of the setParameters() method. More...

void	defaultsToParam_ ()
	Updates the parameters after the defaults have been set in the constructor. More...

Protected Attributes inherited from DefaultParamHandler
Param	param_
	Container for current parameters. More...

Param	defaults_
	Container for default parameters. This member should be filled in the constructor of derived classes! More...

std::vector< String >	subsections_
	Container for registered subsections. This member should be filled in the constructor of derived classes! More...

String	error_name_
	Name that is displayed in error messages during the parameter checking. More...

bool	check_defaults_
	If this member is set to false no checking if parameters in done;. More...

bool	warn_empty_defaults_
	If this member is set to false no warning is emitted when defaults are empty;. More...

Detailed Description

This class holds the functionality of calculating the database suitability.

To calculate the suitability of a database for a specific mzML for identification search, it is vital to perform a combined deNovo+database identification search. Meaning that the database should be appended with an additional entry derived from concatenated deNovo sequences from said mzML. Currently only Comet search is supported.

This class will calculate q-values by itself and will throw an error if any q-value calculation was done beforehand.

The algorithm parameters can be set using setParams().

Allows for multiple usage of the compute function. The result of each call is stored internally in a vector. Therefore old results will not be overridden by a new call. This vector then can be returned using getResults().

This class serves as the library representation of DatabaseSuitability

Class Documentation

◆ OpenMS::DBSuitability::SuitabilityData

struct OpenMS::DBSuitability::SuitabilityData

struct to store results

Collaboration diagram for DBSuitability::SuitabilityData:

[legend]

Class Members
double	cut_off	the cut-off that was used to determine when a score difference was "small enough" this is normalized by mw
Size	num_interest	number of times a deNovo hit scored on top of a database hit
Size	num_re_ranked	number of times a deNovo hit scored on top of a database hit, but their score difference was small enough, that it was still counted as a database hit
Size	num_top_db	number of times the top hit is considered to be a database hit
Size	num_top_novo	number of times the top hit is considered to be a deNovo hit
double	suitability	the suitability of the database used for identification search, calculated with: #db_hits / (#db_hits + #deNovo_hit) can reach from 0 -> the database was not at all suited to 1 -> the perfect database was used Preliminary tests have shown that databases of the right organism or close related organisms score around 0.9 to 0.95, organisms from the same class can still score around 0.8, organisms from the same phylum score around 0.5 to 0.6 and after that it quickly falls to suitabilities of 0.15 or even 0.05. Note that these test were only performed for one mzML and your results might differ.

Constructor & Destructor Documentation

◆ DBSuitability()

DBSuitability ( )

Constructor Settings are initialized with their default values: no_rerank = false, reranking_cutoff_percentile = 1, FDR = 0.01

◆ ~DBSuitability()

~DBSuitability ( )

default

Destructor.

Member Function Documentation

◆ compute()

void compute ( std::vector< PeptideIdentification > pep_ids )

Computes suitability of a database used to search a mzML.

Counts top deNovo and top database hits. The ratio of db hits vs all hits yields the suitability. To re-rank cases, where a de novo peptide scores just higher than the database peptide, a decoy cut-off is calculated. This functionality can be turned off. This will result in an underestimated suitability, but it can solve problems like different search engines or to few decoy hits.

Parameters can be set using the functionality of DefaultParamHandler. Parameters are: no_rerank - re-ranking can be turned off with this reranking_cutoff_percentile - percentile that determines which cut-off will be returned FDR - q-value that should be filtered for Preliminary tests have shown that database suitability is rather stable across common FDR thresholds from 0 - 5 %

Since q-values need to be calculated the identifications are taken by copy.

Result is appended to the result member. This allows for multiple usage.

Parameters

pep_ids vector containing pepIDs with target/decoy annotation coming from a deNovo+database identification search (currently only Comet-support) without FDR vector is modified internally, and is thus copied

Exceptions

MissingInformation	if no target/decoy annotation is found
MissingInformation	if no xcorr is found
Precondition	if a q-value is found in the input

◆ getDecoyCutOff_()

double getDecoyCutOff_	(	const std::vector< PeptideIdentification > &	pep_ids,
		double	reranking_cutoff_percentile
	)

private

Calculates a xcorr cut-off based on decoy hits.

Decoy differences of all N pepIDs are calculated. The (1-reranking_cutoff_percentile)*N highest one is returned. It is assumed that this difference accounts for 'reranking_cutoff_percentile' of the re-ranking cases.

Parameters

pep_ids	vector containing the pepIDs
reranking_cutoff_percentile	percentile that determines which cut-off will be returned

Returns: xcorr cut-off

Exceptions

IllegalArgument	if reranking_cutoff_percentile isn't in range [0,1]
IllegalArgument	if reranking_cutoff_percentile is too low for a decoy cut-off to be calculated
MissingInformation	if no more than 20 % of the peptide IDs have two decoys in their top ten peptide hits

◆ getDecoyDiff_()

double getDecoyDiff_ ( const PeptideIdentification & pep_id )

private

Calculates the xcorr difference between the top two hits marked as decoy.

Only searches the top ten hits for two decoys. If there aren't two decoys, DBL_MAX is returned.

Parameters

pep_id pepID from where the decoy difference will be calculated

Returns: xcorr difference

Exceptions

MissingInformation	if no target/decoy annotation is found
MissingInformation	if no xcorr is found

◆ getResults()

const std::vector<SuitabilityData>& getResults ( ) const

Returns results calculated by this metric.

The returned vector contains one DBSuitabilityData object for each time compute was called. Each of these objects contains the suitability information that was extracted from the identifications used for the corresponding call of compute.

Returns: DBSuitabilityData objects in a vector

◆ isNovoHit_()

bool isNovoHit_ ( const PeptideHit & hit )

private

Tests if a PeptideHit is considered a deNovo hit.

To test this the function looks into the protein accessions. If only the deNovo protein is found, 'true' is returned. If at least one database protein is found, 'false' is returned.

Parameters

hit	PepHit in question

Returns: true/false

◆ passesFDR_()

bool passesFDR_	(	const PeptideHit &	hit,
		double	FDR
	)

private

Tests if a PeptideHit has a lower q-value than the given FDR threshold, i.e. passes FDR.

Q-value is searched at score and at meta-value level.

Parameters

hit	PepHit in question
FDR	FDR threshold to check against

Returns: true/false

Member Data Documentation

◆ results_

std::vector<SuitabilityData> results_

private

result vector

Classes

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Class Documentation

◆ OpenMS::DBSuitability::SuitabilityData

Constructor & Destructor Documentation

◆ DBSuitability()

◆ ~DBSuitability()

Member Function Documentation

◆ compute()

◆ getDecoyCutOff_()

◆ getDecoyDiff_()

◆ getResults()

◆ isNovoHit_()

◆ passesFDR_()

Member Data Documentation

◆ results_