init_report: Function that initiates oncoEnrichR report structure
In sigven/oncoEnrichR: Cancer-dedicated gene set interpretation

View source: R/onco_enrichr.R

init_report

R Documentation

Function that initiates oncoEnrichR report structure

Description

Function that initiates oncoEnrichR report structure

Usage

init_report(
  oeDB,
  project_title = "_Project title_",
  project_owner = "_Project owner_",
  html_floating_toc = T,
  html_report_theme = "default",
  query_id_type = "symbol",
  ignore_id_err = TRUE,
  project_description = "_Project description_",
  ppi_string_min_score = 0.9,
  ppi_string_network_type = "functional",
  ppi_biogrid_min_evidence = 3,
  ppi_add_nodes = 30,
  ppi_show_isolated_nodes = FALSE,
  ppi_node_shadow = TRUE,
  ppi_show_drugs = T,
  bgset_description = "All annotated protein-coding genes",
  bgset_id_type = "symbol",
  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 = F,
  subcellcomp_min_confidence = 3,
  subcellcomp_min_channels = 1,
  subcellcomp_show_cytosol = F,
  regulatory_min_confidence = "D",
  fitness_max_score = -2,
  show_ppi = T,
  show_disease = T,
  show_top_diseases_only = T,
  show_cancer_hallmarks = T,
  show_drug = T,
  show_enrichment = T,
  show_aberration = T,
  show_coexpression = T,
  show_subcell_comp = T,
  show_fitness = T,
  show_cell_tissue = F,
  show_ligand_receptor = T,
  show_regulatory = T,
  show_unknown_function = T,
  show_prognostic = T,
  show_synleth = T,
  show_complex = T,
  show_domain = T
)

Arguments

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