| OpenMS 2.5.0

Public Member Functions | Public Attributes | List of all members
OpenSwath_Scores Struct Reference

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

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

## 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_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 | 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_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_score

double im_ms1_delta_score = 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