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Table 1 Scoring methods offered in FELLA, chosen by the enrich function arguments method and approx

From: FELLA: an R package to enrich metabolomics data

Method

Approx

Notation in [12]

Comment

Hypergeom

N/A

Hypergeometric test

Included for reference

Diffusion

Normality

HD norm

Heat diffusion scores followed by z-scores

Diffusion

Simulation

HD sim

Heat diffusion scores followed by permutations

Pagerank

Normality

PR norm

PageRank scores followed by z-scores

Pagerank

Simulation

PR sim

PageRank scores followed by permutations

  1. Each row corresponds to a method mentioned in the original publication [12]. The method hypergeom is Fisher’s exact test, included for reference. Method diffusion scores the nodes using the heat diffusion model. Method pagerank uses the PageRank algorithm on an upwards-directed version of the network. Both scores undergo a statistical normalisation to remove structural biases, controlled through the approx argument. The user can choose the fast, parametric z-scores (normality) or the slower, non-parametric permutation analysis (simulation). N/A: non-applicable