get_pathway_list_data: Create pathway table with gene sets

In espors/idepGolem: Integrated Differential Expression and Pathway Analysis

Create pathway table with gene sets

Description

Create a data frame of significant pathways and their analysis values. Also add a column that contains the gene sets for the pathway.

Usage

get_pathway_list_data(
  pathway_method,
  gage_pathway_data,
  fgsea_pathway_data,
  pgsea_plot_data,
  pgsea_plot_all_samples_data,
  gsva_plot_data,
  go,
  select_org,
  gene_info,
  gene_sets,
  show_pathway_id
)

Arguments

pathway_method	Integer indicating which pathway method to use. Should be one of 1 for "GAGE", 2 = "PGSEA", 3 for "GSEA (preranded fgsea)", 4 for "PGSEA w/ all samples", and 5 for "ReactomePA".
gage_pathway_data	Matrix returned from gage_data()
fgsea_pathway_data	Matrix returned from fgsea_data()
pgsea_plot_data	Matrix returned from get_pgsea_plot_data()
pgsea_plot_all_samples_data	Matrix returned from get_pgsea_plot_all_samples_data()
go	String designating the section of the database to query for pathway analysis. See gmt_category() for choices.
select_org	String designating which organism is being analyzed
gene_info	Matrix returned from gene_info() function, all gene info from the database query with the User gene IDs
gene_sets	List of vectors with each vector being the set of genes that correspond to a particular pathway in the database read_gene_sets function()
show_pathway_id	whether to show pathway id or remove it

Value

A data frame with the pathway analysis statistics and the gene sets for each significantly enriched pathway.

See Also

Other pathway functions: fgsea_data(), find_overlap(), gage_data(), get_gsva_plot_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()

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