calculate_features: Calculate the default features used to predict interactions...
In fosterlab/PrInCE: Predicting Interactomes from Co-Elution

Calculate the six features that are used to discriminate interacting and non-interacting protein pairs based on co-elution profiles in PrInCE, namely: raw Pearson R value, cleaned Pearson R value, raw Pearson P-value, Euclidean distance, co-peak, and co-apex. Optionally, one or more of these can be disabled.

calculate_features(
  profile_matrix,
  gaussians,
  min_pairs = 0,
  pearson_R_raw = TRUE,
  pearson_R_cleaned = TRUE,
  pearson_P = TRUE,
  euclidean_distance = TRUE,
  co_peak = TRUE,
  co_apex = TRUE,
  n_pairs = FALSE,
  max_euclidean_quantile = 0.9
)

`profile_matrix`	a numeric matrix of co-elution profiles, with proteins in rows, or a `MSnSet` object
`gaussians`	a list of Gaussian mixture models fit to the profile matrix by `link{build_gaussians}`
`min_pairs`	minimum number of overlapping fractions between any given protein pair to consider a potential interaction
`pearson_R_raw`	if true, include the Pearson correlation (R) between raw profiles as a feature
`pearson_R_cleaned`	if true, include the Pearson correlation (R) between cleaned profiles as a feature
`pearson_P`	if true, include the P-value of the Pearson correlation between raw profiles as a feature
`euclidean_distance`	if true, include the Euclidean distance between cleaned profiles as a feature
`co_peak`	if true, include the 'co-peak score' (that is, the distance, in fractions, between the single highest value of each profile) as a feature
`co_apex`	if true, include the 'co-apex score' (that is, the minimum Euclidean distance between any pair of fit Gaussians) as a feature
`max_euclidean_quantile`	very high Euclidean distance values are trimmed to avoid numerical precision issues; values above this quantile will be replaced with the value at this quantile (default: `0.9`)