In sigven/oncoEnrichR: Cancer-dedicated gene set interpretation

Documentation and settings

The configurations set for this oncoEnrichR report are outlined below, in addition to an overview of knowledge resources used.

Configuration values for `onco_enrich()`

General:
html_report_theme = r onc_enrich_report[['config']][['rmarkdown']][['theme']]
html_floating_toc = r onc_enrich_report[['config']][['rmarkdown']][['floating_toc']]
query_id_type = r onc_enrich_report[['config']][['query']][['id_type']]
bgset_id_type = r onc_enrich_report[['config']][['bgset']][['id_type']]
bgset_description = r onc_enrich_report[['config']][['enrichment']][['bgset_description']]
Modules included in report:
show_disease = r onc_enrich_report[['config']][['show']][['disease']]
show_drugs = r onc_enrich_report[['config']][['show']][['drug']]
show_cancer_hallmarks = r onc_enrich_report[['config']][['show']][['cancer_hallmark']]
show_fitness = r onc_enrich_report[['config']][['show']][['fitness']]
show_complex = r onc_enrich_report[['config']][['show']][['protein_complex']]
show_unknown_function = r onc_enrich_report[['config']][['show']][['unknown_function']]
show_domain = r onc_enrich_report[['config']][['show']][['protein_domain']]
show_synleth = r onc_enrich_report[['config']][['show']][['synleth']]
show_ligand_receptor = r onc_enrich_report[['config']][['show']][['ligand_receptor']]
show_regulatory = r onc_enrich_report[['config']][['show']][['regulatory']]
show_subcellcomp = r onc_enrich_report[['config']][['show']][['subcellcomp']]
show_enrichment = r onc_enrich_report[['config']][['show']][['enrichment']]
show_cell_tissue = r onc_enrich_report[['config']][['show']][['cell_tissue']]
show_coexpression = r onc_enrich_report[['config']][['show']][['coexpression']]
show_aberration = r onc_enrich_report[['config']][['show']][['aberration']]
show_prognostic = r onc_enrich_report[['config']][['show']][['cancer_prognosis']]
show_ppi = r onc_enrich_report[['config']][['show']][['ppi']]
Cancer associations:
show_top_diseases_only = r onc_enrich_report[['config']][['disease']][['show_top_diseases']]
Regulatory interactions:
regulatory_min_confidence = r onc_enrich_report[['config']][['regulatory']][['min_confidence']]
Subcellular compartments:
subcellcomp_min_confidence = r onc_enrich_report[['config']][['subcellcomp']][['minimum_confidence']]
subcellcomp_min_channels = r onc_enrich_report[['config']][['subcellcomp']][['minimum_channels']]
subcellcomp_show_cytosol = r onc_enrich_report[['config']][['subcellcomp']][['show_cytosol']]
Gene fitness scores:
fitness_max_score = r onc_enrich_report[['config']][['fitness']][['max_BF_score']]
Enrichment:
enrichment_p_value_cutoff = r onc_enrich_report[['config']][['enrichment']][['p_value_cutoff']]
enrichment_q_value_cutoff = r onc_enrich_report[['config']][['enrichment']][['q_value_cutoff']]
enrichment_p_value_adj = r onc_enrich_report[['config']][['enrichment']][['p_adjust_method']]
enrichment_min_geneset_size = r onc_enrich_report[['config']][['enrichment']][['min_gs_size']]
enrichment_max_geneset_size = r onc_enrich_report[['config']][['enrichment']][['max_gs_size']]
enrichment_simplify_go = r onc_enrich_report[['config']][['enrichment']][['simplify_go']]
enrichment_plot_num_terms = r onc_enrich_report[['config']][['enrichment']][['enrichment_plot_num_terms']]
Protein-protein interactions:
ppi_string_min_score = r onc_enrich_report[['config']][['ppi']][['string']][['minimum_score']]
ppi_string_network_type = r onc_enrich_report[['config']][['ppi']][['string']][['network_type']]
ppi_biogrid_min_evidence = r onc_enrich_report[['config']][['ppi']][['biogrid']][['minimum_evidence']]
ppi_add_nodes = r onc_enrich_report[['config']][['ppi']][['string']][['add_nodes']]
ppi_node_shadow = r onc_enrich_report[['config']][['ppi']][['string']][['visnetwork_shadow']]
ppi_show_drugs = r onc_enrich_report[['config']][['ppi']][['string']][['show_drugs']]
ppi_show_isolated_nodes = r onc_enrich_report[['config']][['ppi']][['string']][['show_isolated_nodes']]

Annotation resources

The analysis performed in the oncoEnrichR report is based on the following main tools and knowledge resources:

Software

for(n in names(onc_enrich_report[['config']][['resources']])){
  if(onc_enrich_report[['config']][['resources']][[n]]$resource_type == 'software'){
    license <- onc_enrich_report[['config']][['resources']][[n]]$license
    s <- glue::glue(
      "    * [{onc_enrich_report[['config']][['resources']][[n]]$name}]",
      "({onc_enrich_report[['config']][['resources']][[n]]$url}) - ", "{onc_enrich_report[['config']][['resources']][[n]]$description} ",  "({onc_enrich_report[['config']][['resources']][[n]]$version}) - ",
      "[{onc_enrich_report[['config']][['resources']][[n]]$license}]",
      "({onc_enrich_report[['config']][['resources']][[n]]$license_url})")
    if(license == "."){
      s <- glue::glue(
        "    * [{onc_enrich_report[['config']][['resources']][[n]]$name}]",
        "({onc_enrich_report[['config']][['resources']][[n]]$url}) - ", "{onc_enrich_report[['config']][['resources']][[n]]$description} ",  "({onc_enrich_report[['config']][['resources']][[n]]$version}) - ",
        "**See below for licensing requirements**")
    }else if(license == "Open Access"){
      s <- glue::glue(
        "    * [{onc_enrich_report[['config']][['resources']][[n]]$name}]",
        "({onc_enrich_report[['config']][['resources']][[n]]$url}) - ", "{onc_enrich_report[['config']][['resources']][[n]]$description} ",  "({onc_enrich_report[['config']][['resources']][[n]]$version}) - ",
        "*Open Access*")
    }
    cat(s,sep="\n")
  }
}

Databases/datasets

for(n in names(onc_enrich_report[['config']][['resources']])){
  if(onc_enrich_report[['config']][['resources']][[n]]$resource_type != 'software'){
    license <- onc_enrich_report[['config']][['resources']][[n]]$license

    s <- glue::glue(
      "    * [{onc_enrich_report[['config']][['resources']][[n]]$name}]",
      "({onc_enrich_report[['config']][['resources']][[n]]$url}) - ", "{onc_enrich_report[['config']][['resources']][[n]]$description} ",  "({onc_enrich_report[['config']][['resources']][[n]]$version}) - ",
      "[{onc_enrich_report[['config']][['resources']][[n]]$license}]",
      "({onc_enrich_report[['config']][['resources']][[n]]$license_url})")
    if(license == "."){
      s <- glue::glue(
        "    * [{onc_enrich_report[['config']][['resources']][[n]]$name}]",
        "({onc_enrich_report[['config']][['resources']][[n]]$url}) - ", "{onc_enrich_report[['config']][['resources']][[n]]$description} ",  "({onc_enrich_report[['config']][['resources']][[n]]$version}) - ",
        "**<sup>\\*</sup>See below for licensing requirements**")
    }else if(license == "Open Access"){
      s <- glue::glue(
        "    * [{onc_enrich_report[['config']][['resources']][[n]]$name}]",
        "({onc_enrich_report[['config']][['resources']][[n]]$url}) - ", "{onc_enrich_report[['config']][['resources']][[n]]$description} ",  "({onc_enrich_report[['config']][['resources']][[n]]$version}) - ",
        "*Open Access*")
    }
    cat(s,sep="\n")

  }
}

cat(glue::glue(
  " <br><br><sup>\\*</sup>*[KEGG]({onc_enrich_report[['config']][['resources']][['kegg']]$url})",
  " and [CGC]({onc_enrich_report[['config']][['resources']][['cgc']]$url}) are freely",
  " available for academic, non-commercial",
  " use. For commercial usage, end users need to consult [https://www.pathway.jp](https://www.pathway.jp/)",
  " and [https://cancer.sanger.ac.uk/cosmic/license](https://cancer.sanger.ac.uk/cosmic/license)",
  " for licensing inquiries.*<br><br>"), sep="\n")