This function calculates the total annotation score based on the matching scores for m/z, retention time (RT), and spectral similarity (SS). The total score is calculated as a weighted sum of these matching scores, with weights determined by the `based_on` argument.
calculate_total_score(
mz.match.score,
RT.match.score,
SS,
ms1.match.weight = 0.25,
rt.match.weight = 0.25,
ms2.match.weight = 0.5,
based_on = c("ms1", "rt", "ms2")
)Numeric vector. The m/z match scores.
Numeric vector. The retention time (RT) match scores.
Numeric vector. The MS2 spectral similarity (SS) scores.
Numeric. The weight assigned to the MS1 (m/z) match score. Default is 0.25.
Numeric. The weight assigned to the RT match score. Default is 0.25.
Numeric. The weight assigned to the MS2 (spectral similarity) match score. Default is 0.5.
Character vector. Specifies the criteria to base the total score on. Can include `"ms1"`, `"rt"`, and/or `"ms2"`. Default is `c("ms1", "rt", "ms2")`.
A numeric vector representing the total score for each match, computed as the weighted sum of m/z, RT, and MS2 scores.
The function calculates the total score by applying weights to the individual match scores (`mz.match.score`, `RT.match.score`, `SS`). If the `based_on` argument specifies only one or two matching criteria (e.g., `"ms1"` or `"ms1"`, `"rt"`), the weights are adjusted accordingly.
The weights for `ms1.match.weight`, `rt.match.weight`, and `ms2.match.weight` must sum to 1. If any of the matching scores (m/z, RT, SS) contain `NA` values, those scores are treated as 0 in the total score calculation.
if (FALSE) { # \dontrun{
# Example matching scores
mz_scores <- c(0.9, 0.8, 0.7)
rt_scores <- c(0.8, 0.7, 0.9)
ss_scores <- c(0.7, 0.9, 0.8)
# Calculate the total score using the default weights
total_scores <- calculate_total_score(
mz.match.score = mz_scores,
RT.match.score = rt_scores,
SS = ss_scores,
based_on = c("ms1", "rt", "ms2")
)
print(total_scores)
} # }