random_probability: Random probability

In diogocamacho/rpegeos: Pathway enrichment for gene expression signatures

Description

This function computes the cosine similarity between the set of randomized gene sets and the pathway tf-idf matrix. It calls the cosine_similarity function and returns the probability of a given cosine similarity being random.

Usage

random_probability(similarity_results, gene_set, fthr, pthr, num_sets,
  target_tfidf, tfidf_crossprod)

Arguments

similarity_results	Vector of cosine similarities
gene_set	Query gene set
fthr	Fold-change threshold for differential expression
pthr	P-value threshold for differential expression
num_sets	Number of random sets to generate
target_tfidf	Pathway tf-idf matrix.
tfidf_crossprod	Cross-product vector for pathway tf-idf.

Value

A vector of random probabilities for each pathway given the gene set size.

diogocamacho/rpegeos documentation built on June 4, 2019, 6:37 p.m.