pgsea_plot_all: Pathway analysis with the PGSEA package on all samples

In espors/idepGolem: Integrated Differential Expression and Pathway Analysis

Pathway analysis with the PGSEA package on all samples

Description

Run pathway analysis with the PGSEA package using the results from the limma_value() on all samples.

Usage

pgsea_plot_all(
  go,
  my_range,
  data,
  select_contrast,
  gene_sets,
  pathway_p_val_cutoff,
  n_pathway_show,
  select_go,
  show_pathway_id,
  margin = c(3, 1, 13, 38),
  plot_colors = NULL
)

Arguments

go	String designating the section of the database to query for pathway analysis. See gmt_category() for choices.
my_range	Vector of the (min_set_size, max_set_size)
data	Matrix of gene data that has been through the 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()
pathway_p_val_cutoff	Significant p-value to determine enriched pathways
n_pathway_show	Number of pathways to return in final result
select_go	pathway category.
show_pathway_id	Whether to show pathway id for GO and KEGG pathways
plot_colors	A vector of colors for activated/surpressed pathways

Value

A data frame with the results of the pathway analysis. The data frame has five columns for the direction of the regulation, the pathway description, the stat value, the number of overlapping genes, and the p-value.

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(), get_pgsea_plot_data(), gsva_data(), kegg_pathway(), pathway_select_data(), pgsea_data(), 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.