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,
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 = FALSE,
show_coexpression = FALSE,
show_ligand_receptor = FALSE,
show_regulatory = FALSE,
show_unknown_function = TRUE,
show_prognostic = TRUE,
show_subcell_comp = FALSE,
show_synleth = FALSE,
show_fitness = TRUE,
show_complex = TRUE,
show_domain = FALSE,
...
)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_transcript_id", "ensembl_protein", "refseq_protein")
- ignore_id_err
logical indicating if analysis should continue when uknown query identifiers are encountered
- 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_transcript_id", "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) #param 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