A structure to hold the different scores computed by OpenSWATH. More...

#include <OpenMS/ANALYSIS/OPENSWATH/OpenSwathScores.h>

Collaboration diagram for OpenSwath_Scores:

Public Member Functions
	OpenSwath_Scores ()=default

double	get_quick_lda_score (double library_corr_, double library_norm_manhattan_, double norm_rt_score_, double xcorr_coelution_score_, double xcorr_shape_score_, double log_sn_score_) const

double	calculate_lda_prescore (const OpenSwath_Scores &scores) const
	A quick LDA model based non-DIA scores. More...

double	calculate_lda_single_transition (const OpenSwath_Scores &scores) const
	A scoring model for peak groups with a single transition. More...

double	calculate_swath_lda_prescore (const OpenSwath_Scores &scores) const
	A full LDA model using DIA and non-DIA scores. More...

Public Attributes
double	elution_model_fit_score = 0

double	library_corr = 0

double	library_norm_manhattan = 0

double	library_rootmeansquare = 0

double	library_sangle = 0

double	norm_rt_score = 0

double	isotope_correlation = 0

double	isotope_overlap = 0

double	massdev_score = 0

double	xcorr_coelution_score = 0

double	xcorr_shape_score = 0

double	yseries_score = 0

double	bseries_score = 0

double	log_sn_score = 0

double	weighted_coelution_score = 0

double	weighted_xcorr_shape = 0

double	weighted_massdev_score = 0

double	ms1_xcorr_coelution_score = -1

double	ms1_xcorr_coelution_contrast_score = 0

double	ms1_xcorr_coelution_combined_score = 0

double	ms1_xcorr_shape_score = -1

double	ms1_xcorr_shape_contrast_score = 0

double	ms1_xcorr_shape_combined_score = 0

double	ms1_ppm_score = 0

double	ms1_isotope_correlation = 0

double	ms1_isotope_overlap = 0

double	ms1_mi_score = -1

double	ms1_mi_contrast_score = 0

double	ms1_mi_combined_score = 0

double	sonar_sn = 0

double	sonar_diff = 0

double	sonar_trend = 0

double	sonar_rsq = 0

double	sonar_shape = 0

double	sonar_lag = 0

double	im_xcorr_coelution_score = 0

double	im_xcorr_shape_score = 0

double	im_delta_score = 0

double	im_ms1_delta_score = 0

double	im_drift = 0

double	im_drift_weighted = 0

double	im_delta = -1

double	im_ms1_contrast_coelution = 0

double	im_ms1_contrast_shape = 0

double	im_ms1_sum_contrast_coelution = 0

double	im_ms1_sum_contrast_shape = 0

double	im_ms1_drift = 0

double	im_ms1_delta = -1

double	library_manhattan = 0

double	library_dotprod = 0

double	intensity = 0

double	total_xic = 0

double	nr_peaks = 0

double	sn_ratio = 0

double	mi_score = 0

double	weighted_mi_score = 0

double	rt_difference = 0

double	normalized_experimental_rt = 0

double	raw_rt_score = 0

double	dotprod_score_dia = 0

double	manhatt_score_dia = 0

Detailed Description

A structure to hold the different scores computed by OpenSWATH.

This struct is used to store the individual OpenSWATH (sub-)scores. It also allows to compute some preliminary quality score for a feature by using a predefined combination of the individual scores determined using LDA.

Constructor & Destructor Documentation

◆ OpenSwath_Scores()

OpenSwath_Scores ( )

default

Member Function Documentation

◆ calculate_lda_prescore()

double calculate_lda_prescore ( const OpenSwath_Scores & scores ) const

A quick LDA model based non-DIA scores.

A quick model LDA average model on which uses only non-DIA scores (library_corr, library_norm_manhattan, norm_rt_score, xcorr_coelution_score, xcorr_shape_score, log_sn_score and elution_model_fit_score).

Returns: A score which is better when more negative

◆ calculate_lda_single_transition()

double calculate_lda_single_transition ( const OpenSwath_Scores & scores ) const

A scoring model for peak groups with a single transition.

Manually derived scoring model for single transition peakgroups, only uses norm_rt_score, log_sn_score, and elution_model_fit_score.

Returns: A score which is better when more negative

◆ calculate_swath_lda_prescore()

double calculate_swath_lda_prescore ( const OpenSwath_Scores & scores ) const

A full LDA model using DIA and non-DIA scores.

A LDA average model which uses all available scores.

Returns: A score which is better when more negative

◆ get_quick_lda_score()

double get_quick_lda_score	(	double	library_corr_,
		double	library_norm_manhattan_,
		double	norm_rt_score_,
		double	xcorr_coelution_score_,
		double	xcorr_shape_score_,
		double	log_sn_score_
	)		const

Member Data Documentation

◆ bseries_score

double bseries_score = 0

◆ dotprod_score_dia

double dotprod_score_dia = 0

◆ elution_model_fit_score

double elution_model_fit_score = 0

◆ im_delta

double im_delta = -1

◆ im_delta_score

double im_delta_score = 0

◆ im_drift

double im_drift = 0

◆ im_drift_weighted

double im_drift_weighted = 0

◆ im_ms1_contrast_coelution

double im_ms1_contrast_coelution = 0

◆ im_ms1_contrast_shape

double im_ms1_contrast_shape = 0

◆ im_ms1_delta

double im_ms1_delta = -1

◆ im_ms1_delta_score

double im_ms1_delta_score = 0

◆ im_ms1_drift

double im_ms1_drift = 0

◆ im_ms1_sum_contrast_coelution

double im_ms1_sum_contrast_coelution = 0

◆ im_ms1_sum_contrast_shape

double im_ms1_sum_contrast_shape = 0

◆ im_xcorr_coelution_score

double im_xcorr_coelution_score = 0

◆ im_xcorr_shape_score

double im_xcorr_shape_score = 0

◆ intensity

double intensity = 0

◆ isotope_correlation

double isotope_correlation = 0

◆ isotope_overlap

double isotope_overlap = 0

◆ library_corr

double library_corr = 0

◆ library_dotprod

double library_dotprod = 0

◆ library_manhattan

double library_manhattan = 0

◆ library_norm_manhattan

double library_norm_manhattan = 0

◆ library_rootmeansquare

double library_rootmeansquare = 0

◆ library_sangle

double library_sangle = 0

◆ log_sn_score

double log_sn_score = 0

◆ manhatt_score_dia

double manhatt_score_dia = 0

◆ massdev_score

double massdev_score = 0

◆ mi_score

double mi_score = 0

◆ ms1_isotope_correlation

double ms1_isotope_correlation = 0

◆ ms1_isotope_overlap

double ms1_isotope_overlap = 0

◆ ms1_mi_combined_score

double ms1_mi_combined_score = 0

◆ ms1_mi_contrast_score

double ms1_mi_contrast_score = 0

◆ ms1_mi_score

double ms1_mi_score = -1

◆ ms1_ppm_score

double ms1_ppm_score = 0

◆ ms1_xcorr_coelution_combined_score

double ms1_xcorr_coelution_combined_score = 0

◆ ms1_xcorr_coelution_contrast_score

double ms1_xcorr_coelution_contrast_score = 0

◆ ms1_xcorr_coelution_score

double ms1_xcorr_coelution_score = -1

◆ ms1_xcorr_shape_combined_score

double ms1_xcorr_shape_combined_score = 0

◆ ms1_xcorr_shape_contrast_score

double ms1_xcorr_shape_contrast_score = 0

◆ ms1_xcorr_shape_score

double ms1_xcorr_shape_score = -1

◆ norm_rt_score

double norm_rt_score = 0

◆ normalized_experimental_rt

double normalized_experimental_rt = 0

◆ nr_peaks

double nr_peaks = 0

◆ raw_rt_score

double raw_rt_score = 0

◆ rt_difference

double rt_difference = 0

◆ sn_ratio

double sn_ratio = 0

◆ sonar_diff

double sonar_diff = 0

◆ sonar_lag

double sonar_lag = 0

◆ sonar_rsq

double sonar_rsq = 0

◆ sonar_shape

double sonar_shape = 0

◆ sonar_sn

double sonar_sn = 0

◆ sonar_trend

double sonar_trend = 0

◆ total_xic

double total_xic = 0

◆ weighted_coelution_score

double weighted_coelution_score = 0

◆ weighted_massdev_score

double weighted_massdev_score = 0

◆ weighted_mi_score

double weighted_mi_score = 0

◆ weighted_xcorr_shape

double weighted_xcorr_shape = 0

◆ xcorr_coelution_score

double xcorr_coelution_score = 0

◆ xcorr_shape_score

double xcorr_shape_score = 0

◆ yseries_score

double yseries_score = 0

Public Member Functions

Public Attributes