DBSuitability::SuitabilityData Struct Reference

struct to store results More...

#include <OpenMS/QC/DBSuitability.h>

Collaboration diagram for DBSuitability::SuitabilityData:

Public Member Functions
void	clear ()
void	setCorrectionFactor (double factor)
double	getCorrectionFactor () const
double	getCorrectedNovoHits () const
double	getCorrectedSuitability () const
SuitabilityData	simulateNoReRanking () const
	Returns a SuitabilityData object containing the data if re-ranking didn't happen. More...

Public Attributes
Size	num_top_novo = 0
	number of times the top hit is considered to be a deNovo hit More...
Size	num_top_db = 0
	number of times the top hit is considered to be a database hit More...
Size	num_interest = 0
	number of times a deNovo hit scored on top of a database hit More...
Size	num_re_ranked = 0
double	cut_off = DBL_MAX
double	suitability = 0
double	suitability_no_rerank = 0
double	suitability_corr_no_rerank = 0
	the suitability after correcting the top deNovo hits, if re-ranking would have been disabled More...

Private Attributes
double	corr_factor
double	num_top_novo_corr = 0
	number of top deNovo hits multiplied by the correction factor More...
double	suitability_corr = 0

Detailed Description

struct to store results

Member Function Documentation

clear()

void clear

(

)

getCorrectedNovoHits()

double getCorrectedNovoHits

(

)

const

getCorrectedSuitability()

double getCorrectedSuitability

(

)

const

getCorrectionFactor()

double getCorrectionFactor

(

)

const

setCorrectionFactor()

void setCorrectionFactor

(

double

factor

)

apply a correction factor to the already calculated suitability only works if num_top_db and num_top_novo contain a non-zero value

simulateNoReRanking()

SuitabilityData simulateNoReRanking

(

)

const

Returns a SuitabilityData object containing the data if re-ranking didn't happen.

Cases that are re-ranked are already counted. To get the 'no re-ranking' data these cases need to be subtracted from the number of top database hits and added to the number of top deNovo hits.

Returns

simulated suitability data where re-ranking didn't happen

Member Data Documentation

corr_factor

double corr_factor

private

#IDs with only deNovo search / #IDs with only database search used for correcting the number of deNovo hits worse databases will have less IDs than good databases this punishes worse databases more than good ones and will result in a worse suitability

cut_off

double cut_off = DBL_MAX

the cut-off that was used to determine when a score difference was "small enough" this is normalized by mw

num_interest

Size num_interest = 0

number of times a deNovo hit scored on top of a database hit

num_re_ranked

Size num_re_ranked = 0

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

num_top_db

Size num_top_db = 0

number of times the top hit is considered to be a database hit

num_top_novo

Size num_top_novo = 0

number of times the top hit is considered to be a deNovo hit

num_top_novo_corr

double num_top_novo_corr = 0

private

number of top deNovo hits multiplied by the correction factor

suitability

double suitability = 0

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.

suitability_corr

double suitability_corr = 0

private

the suitability after correcting the top deNovo hits to impact worse databases more

The corrected suitability has a more linear behaviour. It basicly translates to the ratio of the theoretical perfect database the used database corresponds to. (i.e. a corrected suitability of 0.5 means the used database contains half the proteins of the 'perfect' database)

suitability_corr_no_rerank

double suitability_corr_no_rerank = 0

the suitability after correcting the top deNovo hits, if re-ranking would have been disabled

suitability_no_rerank

double suitability_no_rerank = 0

the suitability if re-ranking would have been turned off if re-ranking is actually turned off, this will be the same as the normal suitability