pathway_select_data: Get data from genes in selected pathway

View source: R/fct_06_pathway.R

pathway_select_dataR Documentation

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