View source: R/fct_analysis_random.R
find_overlap | R Documentation |
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.
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"
)
pathway_table |
Data frame of results from
|
query_set |
Vector of IDs that the enrichment
analysis should be performed on. This list is also returned from
|
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
|
processed_data |
Matrix of gene data that has been through
|
gene_info |
The gene info from the converted IDs from
|
go |
String designating the section of the database to query for pathway
analysis. See |
idep_data |
List of data returned from |
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. |
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()
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