get_pgsea_plot_data: Data from PGSEA plot

In espors/idepGolem: Integrated Differential Expression and Pathway Analysis

Data from PGSEA plot

Description

Get the data matrix that is plotted in the heatmap created by the plot_pgsea().

Usage

get_pgsea_plot_data(
  my_range,
  data,
  select_contrast,
  gene_sets,
  sample_info,
  select_factors_model,
  select_model_comprions,
  pathway_p_val_cutoff,
  n_pathway_show
)

Arguments

my_range	Vector of the (min_set_size, max_set_size)
data	Matrix of gene data that has been through pre_process()
select_contrast	String designating the comparison from DEG analysis to filter for the significant genes. See the 'comparison' element from the list returned from limma_value() for options.
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 read_gene_sets()
sample_info	Matrix of experiment design information for grouping
select_factors_model	The selected factors for the model expression
select_model_comprions	String designating selected comparisons to analyze in the DEG analysis. See list_model_comparisons_ui() for options
pathway_p_val_cutoff	Significant p-value to determine enriched pathways
n_pathway_show	Number of pathways to return in final result

Value

Data matrix with the rownames the descriptions of pathways and the matrix the returned expression calculation from the PGSEA package.

See Also

Other pathway functions: fgsea_data(), find_overlap(), gage_data(), get_gsva_plot_data(), get_pathway_list_data(), get_pgsea_plot_all_samples_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.