onco_enrich: Interrogate a gene list for cancer relevance

In sigven/oncoEnrichR: Cancer-dedicated gene set interpretation

Interrogate a gene list for cancer relevance

Description

Function that interrogates a list of human gene identifiers for cancer relevance. Multiple perspectives are offered, including tumor aberration and co-expression patterns, druggability, protein-protein interactions, gene fitness effects, regulatory interactions, subcellular compartment enrichment, pathway enrichment, synthetic lethality interactions, prognostic associations, and more.

Usage

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,
  ...
)

Arguments

query	character vector with gene/query identifiers (minimum 2, maximum 1000)
oeDB	oncoEnrichR data repository object - as returned from load_db()
query_id_type	character indicating source of query (one of "uniprot_acc", "symbol","entrezgene", or "ensembl_gene", "ensembl_mrna", "refseq_mrna", "ensembl_protein", "refseq_protein")
ignore_id_err	logical indicating if analysis should continue when uknown query identifiers are encountered
html_floating_toc	logical - float the table of contents to the left of the main document content (HTML report). The floating table of contents will always be visible even when the document is scrolled
html_report_theme	Bootswatch theme for HTML report (any of "bootstrap", "cerulean", "cosmo", "default", "flatly", "journal", "lumen", "paper", "sandstone", "simplex", "spacelab", "united", "yeti")
project_title	project title (title of report)
project_owner	name of project owner
project_description	project background information
bgset	character vector with gene identifiers, used as reference/background for enrichment/over-representation analysis
bgset_id_type	character indicating source of background ("uniprot_acc", "symbol", "entrezgene", "ensembl_gene", "ensembl_mrna", "refseq_mrna", "ensembl_protein", "refseq_protein"), default: "symbol"
bgset_description	character indicating type of background (e.g. "All lipid-binding proteins (n = 200)")
enrichment_p_value_cutoff	cutoff p-value for enrichment/ over-representation analysis (default: 0.05)
enrichment_p_value_adj	one of "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none" (clusterProfiler, default: "BH")
enrichment_q_value_cutoff	cutoff q-value for enrichment analysis (clusterProfiler, default: 0.2)
enrichment_min_geneset_size	minimal size of geneset annotated by term for testing in enrichment/over-representation analysis (clusterProfiler, default: 10)
enrichment_max_geneset_size	maximal size of geneset annotated by term for testing in enrichment/over-representation analysis (clusterProfiler, default: 500)
enrichment_plot_num_terms	number of top enriched Gene Ontology terms (max) to show in enrichment barplot (default: 15)
enrichment_simplify_go	remove highly similar GO terms in results from GO enrichment/over-representation analysis (default: TRUE)
subcellcomp_min_confidence	minimum confidence level for subcellular compartment annotation in COMPARTMENTS (min = 3, max = 5, default: 3)
subcellcomp_min_channels	minimum number of channels that support a subcellular compartment annotation in COMPARTMENTS (min = 1, max = 3, default: 1)
subcellcomp_show_cytosol	logical indicating if subcellular heatmap should show highlight proteins located in the cytosol or not (default: FALSE)
regulatory_min_confidence	minimum confidence level for regulatory interactions (TF-target) retrieved from DoRothEA ('A','B','C', or 'D', default: 'D')
fitness_max_score	maximum loss-of-fitness score (scaled Bayes factor from BAGEL) for genes retrieved from DepMap/Project Score, default:-2
ppi_add_nodes	number of nodes to add to target set when computing the protein-protein interaction network (STRING/BioGRID, default: 30)
ppi_string_min_score	minimum score (between 0 and 1) for confidence of retrieved protein-protein interactions (STRING, default: 0.9)
ppi_string_network_type	type of network to show for interactions in STRING ('functional' or 'physical', default: 'functional')
ppi_biogrid_min_evidence	minimum number of evidence items required for protein-protein interactions retrieved (BioGRID, default: 3)
ppi_node_shadow	show shadow for nodes in the displayed PPI network (default: TRUE)
ppi_show_drugs	logical indicating if targeted drugs (>= phase 3) should be displayed in protein-protein interaction networks (default: TRUE)
ppi_show_isolated_nodes	logical indicating if targets/nodes without any interactions should be displayed in the protein-protein interaction networks (default: FALSE)
show_ppi	logical indicating if report should contain protein-protein interaction views of the query set (STRING and BioGRID, default: TRUE)
show_disease	logical indicating if report should contain disease associations (Open Targets Platform, association_score >= 0.05, support from at least two data types), and tumor suppressor/oncogene annotations ( default: TRUE)
show_top_diseases_only	logical indicating if report should contain top (n = 20) disease associations only pr. query gene default: TRUE)
show_cancer_hallmarks	logical indicating if report should contain annotations/evidence of cancer hallmarks per query gene (COSMIC/Open Targets Platform, default: TRUE
show_drug	logical indicating if report should contain targeted cancer drug information (default: TRUE)
show_enrichment	logical indicating if report should contain functional enrichment/over-representation analysis (MSigDB, GO, KEGG, REACTOME, NetPath, WikiPathways, default: TRUE)
show_aberration	logical indicating if report should contain TCGA aberration plots (amplifications/deletions, default: TRUE)
show_coexpression	logical indicating if report should contain TCGA co-expression data (RNAseq) of query set with oncogenes/tumor suppressor genes (default: TRUE)
show_cell_tissue	logical indicating if report should contain tissue-specificity and single cell-type specificity assessments (Human Protein Atlas) of target genes (default: FALSE)
show_ligand_receptor	logical indicating if report should contain ligand-receptor interactions (CellChatDB, default: TRUE)
show_regulatory	logical indicating if report should contain data on transcription factor (TF) - target interactions relevant for the query set (DoRothEA, default: TRUE)
show_unknown_function	logical indicating if report should highlight target genes with unknown or poorly defined functions (GO/Uniprot KB/NCBI, default: TRUE)
show_prognostic	logical indicating if mRNA-based (single-gene) prognostic associations to cancer types should be listed (Human Protein Atlas/TCGA, default: TRUE
show_subcell_comp	logical indicating if report should provide subcellular compartment annotations (COMPARTMENTS, default: TRUE)
show_synleth	logical indicating if report should list overlap with predicted synthetic lethality interactions (gene paralogs only, De Kegel et al., Cell Systems, 2021). Default: TRUE
show_fitness	logical indicating if report should provide fitness scores and target priority scores from CRISPR/Cas9 loss-of-fitness screens (DepMap/Project Score, default: TRUE)
show_complex	logical indicating if report should provide target memberships in known protein complexes (ComplexPortal/Compleat/hu.MAP2/PDB/CORUM, default: TRUE)
show_domain	logical indicating if report should provide target memberships in known protein domains (Pfam, default: TRUE)
...	arguments for Galaxy/web-based processing

Value

An oncoEnrichR report list object, with two main elements, data and config. data contains data that goes into each section of the output reports, config contains all metadata for annotation resources used.

sigven/oncoEnrichR documentation built on Aug. 31, 2023, 8:05 a.m.