pathway_select_data: Get data from genes in selected pathway

In espors/idepGolem: Integrated Differential Expression and Pathway Analysis

Get data from genes in selected pathway

Description

Return a data matrix that is a subset of the processed data and only contains genes that are in the gene set of the desired pathway.

Usage

pathway_select_data(
  sig_pathways,
  gene_sets,
  contrast_samples,
  data,
  select_org,
  all_gene_names
)

Arguments

sig_pathways	Description of the pathway for which to obtain the gene expression data
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()
contrast_samples	Vector of sample columns that correspond to the selected comparison
data	Matrix of gene data that has been through pre_process()
select_org	String designating the organism being analyzed
all_gene_names	Matrix of all the matched and converted gene IDs from get_all_gene_names()

Value

Sub-data matrix from the processed data. Only contains genes from the selected pathway and samples that correspond to the comparison being analyzed.

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(), 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.