find_overlap: Find overlap for pathway analysis
In espors/idepGolem: Integrated Differential Expression and Pathway Analysis

find_overlap

R Documentation

Find overlap for pathway analysis

Description

Use the pathway table element from the list returned from from the read_pathway_sets()to calculate adjusted p-values. Adjusted p-values determine the enriched pathways from the selected query.

Usage

find_overlap(
  pathway_table,
  query_set,
  total_genes,
  processed_data,
  gene_info,
  go,
  idep_data,
  use_filtered_background,
  select_org,
  reduced = FALSE,
  max_terms = 15,
  sort_by_fold = "FALSE"
)

Arguments

`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.
`query_set`	Vector of IDs that the enrichment analysis should be performed on. This list is also returned from `read_pathway_sets()`.
`total_genes`	Length of the query set subtracted from the total number of genes in the database. Could change within the function if the background set changes to the filtered genes.This number is also return from `read_pathway_sets()`.
`processed_data`	Matrix of gene data that has been through `pre_process()`
`gene_info`	The gene info from the converted IDs from `gene_info()`
`go`	String designating the section of the database to query for pathway analysis. See `gmt_category()` for choices.
`idep_data`	List of data returned from `get_idep_data()`
`use_filtered_background`	TRUE/FALSE to indicate the use of the genes that passed the pre_process filter as the background
`select_org`	String designating which organism is being analyzed.
`reduced`	TRUE/FALSE to indicate if function should remove gene sets that are redundant from the final result
`max_terms`	Integer indicating how many pathways to return. Must be a number between 1 and 100. The default is 15.
`sort_by_fold`	TRUE/FALSE indicating if the returned table should be sorted by LFC.

Value

A data frame. If there is significant enrichment, the data frame that is returned has a pathway for each row with the total genes in the database mapping to it as well as the number of genes in the query that map to it. It also contains a column for the p-value and a list of the specific IDs included in the pathway from the query.

Other pathway functions: fgsea_data(), gage_data(), get_gsva_plot_data(), get_pathway_list_data(), get_pgsea_plot_all_samples_data(), get_pgsea_plot_data(), gsva_data(), kegg_pathway(), pathway_select_data(), pgsea_data(), pgsea_plot_all(), plot_gsva(), plot_pgsea(), reactome_data(), remove_pathway_id(), remove_pathway_id_second()