read_pathway_sets: Read pathway sets for gene query

In espors/idepGolem: Integrated Differential Expression and Pathway Analysis

Read pathway sets for gene query

Description

This function provides the gene set information to perform enrichment analysis on the provided query.

Usage

read_pathway_sets(
  all_gene_names_query,
  converted,
  go,
  select_org,
  gmt_file,
  idep_data,
  gene_info
)

Arguments

all_gene_names_query	Subsetted data frame of genes names from get_all_gene_names() to query database with.
converted	List of conversion information on the original IDs returned from the convert_id().
go	String designating the section of the database to query for pathway analysis. See gmt_category() for choices.
select_org	String designating what organism is being analyzed.
gmt_file	For NEW species the gmt file to use for the pathway analysis
idep_data	Data built in to idep
gene_info	The gene info from the converted IDs and the function gene_info()

Value

This function returns a list with values that are used in the find_overlap function. The list contains pathway_table which is the overlap and total genes for each pathway that is enriched in the query. The list also contains the query_set of genes, the total_genes number which is used in the calculation of the p-values and the pathway files that contain gmt information on the mathced species.

espors/idepGolem documentation built on Oct. 27, 2024, 4:56 a.m.