View source: R/fct_06_pathway.R
get_pgsea_plot_all_samples_data | R Documentation |
Get the data matrix that is plotted in the heatmap created by the pgsea_plot_all function.
get_pgsea_plot_all_samples_data(
data,
select_contrast,
gene_sets,
my_range,
pathway_p_val_cutoff,
n_pathway_show
)
data |
Matrix of gene data that has been through
|
select_contrast |
String designating the comparison from DEG analysis to
filter for the significant genes. See the 'comparison' element from the list
returned from |
gene_sets |
List of vectors with each vector being the
set of genes that correspond to a particular pathway in
the database. See list returned 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 pathways to return in final result |
Data matrix with the rownames the descriptions of pathways and the matrix the returned expression calculation from the PGSEA package.
Other pathway functions:
fgsea_data()
,
find_overlap()
,
gage_data()
,
get_gsva_plot_data()
,
get_pathway_list_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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