Skip to contents

Running

Source: vignettes/running.Rmd
running.Rmd

Key functions

oncoEnrichR performs its operations through the following three functions:

1. oncoEnrichR::load_db()

  • Loads the underlying annotation data repository for oncoEnrichR, and saves it to a local cache directory. Utilizing the googledrive R package


2. oncoEnrichR::onco_enrich()

  • Consists of two main processing steps:

    1) Takes an input/query list of human gene/protein identifiers (e.g. UniProt accession, RefSeq/Ensembl transcript identifer etc.) as input and conducts uniform identifier conversion

    2) Performs extensive annotation, enrichment and membership analyses of the query set against underlying data sources on cancer-relevant properties of human genes and their interrelationships.

  • Technically, the method returns a list object with all contents of the analyses performed. The specific arguments/options and default values are outlined below:

    onco_enrich(
  query = NULL,
  oeDB = NULL,
  query_id_type = "symbol",
  ignore_id_err = TRUE,
  html_floating_toc = T,
  html_report_theme = "default",
  project_title = "_Project title_",
  project_owner = "_Project owner_",
  project_description = "_Project description_",
  bgset = NULL,
  bgset_id_type = "symbol",
  bgset_description = "All protein-coding genes",
  enrichment_p_value_cutoff = 0.05,
  enrichment_p_value_adj = "BH",
  enrichment_q_value_cutoff = 0.2,
  enrichment_min_geneset_size = 10,
  enrichment_max_geneset_size = 500,
  enrichment_plot_num_terms = 20,
  enrichment_simplify_go = TRUE,
  subcellcomp_min_confidence = 3,
  subcellcomp_min_channels = 1,
  subcellcomp_show_cytosol = FALSE,
  regulatory_min_confidence = "D",
  fitness_max_score = -2,
  ppi_add_nodes = 30,
  ppi_string_min_score = 0.9,
  ppi_string_network_type = "functional",
  ppi_biogrid_min_evidence = 3,
  ppi_node_shadow = TRUE,
  ppi_show_drugs = TRUE,
  ppi_show_isolated_nodes = FALSE,
  show_ppi = TRUE,
  show_disease = TRUE,
  show_top_diseases_only = TRUE,
  show_cancer_hallmarks = TRUE,
  show_drug = TRUE,
  show_enrichment = TRUE,
  show_aberration = TRUE,
  show_coexpression = TRUE,
  show_cell_tissue = FALSE,
  show_ligand_receptor = TRUE,
  show_regulatory = TRUE,
  show_unknown_function = TRUE,
  show_prognostic = TRUE,
  show_subcell_comp = TRUE,
  show_synleth = TRUE,
  show_fitness = TRUE,
  show_complex = TRUE,
  show_domain = TRUE)

    See detailed descriptions of all options here


3. oncoEnrichR::write()

  • Consists of two main processing steps:

    1) Transformation of the raw analysis results returned by oncoEnrichR::onco_enrich() into various visualizations and interactive tables

    2) Assembly and generation of the final analysis report through

    • A) a structured and interactive oncoEnrichR HTML report
    • B) a multisheet Excel workbook


Example run

A target list of n = 134 high-confidence interacting proteins with the c-MYC oncoprotein were previously identified through BioID protein proximity assay in standard cell culture and in tumor xenografts (Dingar et al., J Proteomics, 2015). We ran this target list through the oncoEnrichR analysis workflow using the following configurations for the onco_enrich method:

  • project_title = "cMYC_BioID_screen"
  • project_owner = "Raught et al."

and produced the following HTML report with results.

Below are R commands provided to reproduce the example output. NOTE: Replace “LOCAL_FOLDER” with a directory on your local computer:

  • library(oncoEnrichR)
  • myc_interact_targets <- read.csv(system.file("extdata","myc_data.csv", package = "oncoEnrichR"), stringsAsFactors = F)
  • oeDB <- oncoEnrichR::load_db(cache_dir = "LOCAL_FOLDER")
  • myc_report <- oncoEnrichR::onco_enrich(query = myc_interact_targets$symbol, oeDB = oeDB, show_cell_tissue = T, project_title = "cMYC_BioID_screen", project_owner = "Raught et al.")
  • oncoEnrichR::write(report = myc_report, oeDB = oeDB, file = "LOCAL_FOLDER/myc_report_oncoenrichr.html", format = "html")
  • oncoEnrichR::write(report = myc_report, oeDB = oeDB, file = "LOCAL_FOLDER/myc_report_oncoenrichr.xlsx", format = "excel")