enrich_geneset: rPEGEOS wrapper

In diogocamacho/rpegeos: Pathway enrichment for gene expression signatures

Description

This function is a wrapper for a start to finish pathway enrichment analysis using tf-idf. For a given gene set of interest, the algorithm will compute the cosine similarity between this vector and the gene sets in a given collection of pathways (for example, KEGG pathways.) Additionally, the algorithm will generate a set of random gene sets that will be used to determine the probability of a given enrichment being random. The output of the wrapper is a tidy data frame with all the enrichment scores that are better than 0.

Usage

enrich_geneset(gene_set)

Arguments

gene_set

Query gene set of interest. Should be a Nx3 matrix, where column 1 is Entrez ID, column 2 is fold-change, and column 3 is p-value (recommend using FDR corrected p-values from a package like 'limma' or 'DESeq2')

Value

A tibble with columns geneset, number_genes, cosine_similarity, and probability_random.

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