calculate_features {PrInCE} | R Documentation

## Calculate the default features used to predict interactions in PrInCE

### Description

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.

### Usage

    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
    )

### Arguments

`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`)

### Value

a data frame containing the calculated features for all possible protein pairs

[Package PrInCE version 1.10.0 Index]