read_gene_sets: Read pathway gene sets

In espors/idepGolem: Integrated Differential Expression and Pathway Analysis

Read pathway gene sets

Description

Use the IDs from the converted database to find the gene sets for all the pathways in the database. Returns a list with each entry a vector of IDs corresponding to a description of a pathway in the database.

Usage

read_gene_sets(converted, all_gene_names, go, select_org, idep_data, my_range)

Arguments

converted	List of converted gene information from convert_id()
all_gene_names	Data frame of gene names from get_all_gene_names()
go	String designating the section of the database to query for pathway analysis. See gmt_category() for choices.
select_org	String designating with organism is being analyzed
idep_data	List of data returned from get_idep_data()
my_range	Vector of the (min_set_size, max_set_size)

Value

A list with each entry a list of gene IDs that correspond to a pathway.

espors/idepGolem documentation built on April 23, 2024, 1:11 p.m.