get_pgsea_plot_all_samples_data: Data from PGSEA plot all samples

View source: R/fct_06_pathway.R

get_pgsea_plot_all_samples_dataR Documentation

Data from PGSEA plot all samples

Description

Get the data matrix that is plotted in the heatmap created by the pgsea_plot_all function.

Usage

get_pgsea_plot_all_samples_data(
  data,
  select_contrast,
  gene_sets,
  my_range,
  pathway_p_val_cutoff,
  n_pathway_show
)

Arguments

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()

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

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_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 Oct. 27, 2024, 4:56 a.m.