fetch_gene_set {pathfindR}

Fetch Gene Set Objects

Description

Function for obtaining the gene sets per term and the term descriptions to be used for enrichment analysis.

Usage

fetch_gene_set(
  gene_sets = "KEGG",
  min_gset_size = 10,
  max_gset_size = 300,
  custom_genes = NULL,
  custom_descriptions = NULL
)

Arguments

gene_sets

Name of the gene sets to be used for enrichment analysis. Available gene sets are 'KEGG', 'Reactome', 'BioCarta', 'GO-All', 'GO-BP', 'GO-CC', 'GO-MF', 'cell_markers', 'mmu_KEGG' or 'Custom'. If 'Custom', the arguments custom_genes and custom_descriptions must be specified. (Default = 'KEGG')

min_gset_size

minimum number of genes a term must contain (default = 10)

max_gset_size

maximum number of genes a term must contain (default = 300)

custom_genes

a list containing the genes involved in each custom term. Each element is a vector of gene symbols located in the given custom term. Names should correspond to the IDs of the custom terms.

custom_descriptions

A vector containing the descriptions for each custom term. Names of the vector should correspond to the IDs of the custom terms.

Value

a list containing 2 elements

genes_by_term

list of vectors of genes contained in each term

term_descriptions

vector of descriptions per each term

Examples

KEGG_gset <- fetch_gene_set()
GO_MF_gset <- fetch_gene_set('GO-MF', min_gset_size = 20, max_gset_size = 100)