View source: R/fct_06_pathway.R
pgsea_data | R Documentation |
Run pathway analysis with the PGSEA package using the results from the limma_value function.
pgsea_data(
processed_data,
gene_sets,
my_range,
pathway_p_val_cutoff,
n_pathway_show
)
processed_data |
Matrix of gene data that has been through
|
gene_sets |
List of vectors with each vector being the
set of genes that correspond to a particular pathway in
the database. See returned list from |
my_range |
Vector of the (min_set_size, max_set_size) |
pathway_p_val_cutoff |
Significant p-value to determine enriched pathways |
n_pathway_show |
Number of significant pathways to show |
A list with a data frame and a numeric value that is used
in the plot_pgsea()
to create a heatmap.
Other pathway functions:
fgsea_data()
,
find_overlap()
,
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_plot_all()
,
plot_gsva()
,
plot_pgsea()
,
reactome_data()
,
remove_pathway_id()
,
remove_pathway_id_second()
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