get_gsva_plot_data: Data from GSVA plot

In espors/idepGolem: Integrated Differential Expression and Pathway Analysis

Data from GSVA plot

Description

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

Usage

get_gsva_plot_data(
  my_range,
  data,
  select_contrast,
  gene_sets,
  sample_info,
  select_factors_model,
  select_model_comprions,
  pathway_p_val_cutoff,
  n_pathway_show,
  algorithm = "gsva"
)

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
algorithm	Options for GSVA: plage, ssgsea, zscore or gsva 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_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()

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