Generate the random, permuted embedding — generate_permuted

This function will generate generate permuted subgraphs that show the same node degree and run the node2vec algorithm on top of these subgraphs. The cosine distance between the real edges will be calculated and stored in the object. These will be used subsequently for statistical significance testing. For more details, please refer to Ietswaart, et al. The function will return a warning and the class as is if you have not run generate_initial_emb().

Usage

generate_permuted_emb(object, n_perm = 3L, seed = 42L, .verbose = TRUE)

Arguments

object: The GeneWalk class, please see GeneWalk().
n_perm: Inter. Number of permutations to generate. Defaults to 3L, the recommendation of the authors.
seed: Integer. Seed for reproducibility.
.verbose: Boolean. Controls verbosity of the function

Value

The object with the added random embeddings for statistical testing.

Details

The function will be using the same parameters for the node2vec training as were used for generate_initial_emb().

References

Ietswaart, et al., Genome Biol, 2021