pathfindR (version 2.1.0)

fetch_gene_set: 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
)

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

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.

Examples

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