background_pathway_sets: Background gene pathway sets

In espors/idepGolem: Integrated Differential Expression and Pathway Analysis

Background gene pathway sets

Description

This function reads the pathway sets for the filtered gene IDs and performs pathway analysis for the query with the filtered background.

Usage

background_pathway_sets(
  processed_data,
  gene_info,
  sub_query,
  go,
  pathway_table,
  idep_data,
  select_org
)

Arguments

processed_data	Matrix of gene data that has been through pre_process()
gene_info	Dataframe of converted IDs information from the function gene_info()
sub_query	Vector of IDs that the enrichment analysis should be performed on. This list is also returned from read_pathway_sets().
go	String designating the section of the database to query for pathway analysis. See gmt_category() for choices.
pathway_table	Data frame of results from read_pathway_sets(). If this data frame is NULL or 0 rows there this function will return no significant enrichment.
idep_data	List of data returned from get_idep_data()
select_org	Species selected.

Value

Pathway gene set table for the background genes. Used in find_overlap to calculate pvals for the filtered background

See Also

This function is used internally in find_overlap()

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