onco_enrich: Function that interrogates and analyzes a list of human...

In sigven/oncoEnrichR: Functional annotation and enrichment analysis of genesets in the context of cancer

Description

Function that interrogates and analyzes a list of human protein-coding genes for cancer relevance

Usage

onco_enrich(
  query,
  query_id_type = "symbol",
  ignore_id_err = FALSE,
  project_title = "Project title",
  project_owner = "Project owner",
  project_description = "Project description",
  bgset = NULL,
  bgset_id_type = "symbol",
  bgset_description = "All protein-coding genes",
  p_value_cutoff_enrichment = 0.05,
  p_value_adjustment_method = "BH",
  q_value_cutoff_enrichment = 0.2,
  min_geneset_size = 10,
  max_geneset_size = 500,
  min_subcellcomp_confidence = 1,
  simplify_go = F,
  ppi_add_nodes = 50,
  ppi_score_threshold = 900,
  show_ppi = T,
  show_drugs_in_ppi = F,
  show_disease = T,
  show_drug = T,
  show_enrichment = T,
  show_tcga_aberration = T,
  show_tcga_coexpression = T,
  show_cell_tissue = T,
  show_unknown_function = T,
  show_prognostic_cancer_assoc = T,
  show_subcell_comp = T,
  show_crispr_lof = T,
  show_complex = T
)

Arguments

query	character vector with gene/query identifiers
query_id_type	character indicating source of query (one of "uniprot_acc", "symbol", "entrezgene", or "ensembl_gene_id")
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_id")
bgset_description	character indicating type of background (e.g. "All lipid-binding proteins (n = 200)")
p_value_cutoff_enrichment	cutoff p-value for enrichment/over-representation analysis
p_value_adjustment_method	one of "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none"
q_value_cutoff_enrichment	cutoff q-value for enrichment analysis
min_geneset_size	minimal size of geneset annotated by term for testing in enrichment/over-representation analysis
max_geneset_size	maximal size of geneset annotated by term for testing in enrichment/over-representation analysis
min_subcellcomp_confidence	minimum confidence level of subcellular compartment annotations (range from 1 to 6, 6 is strongest)
simplify_go	remove highly similar GO terms in results from GO enrichment/over-representation analysis
ppi_add_nodes	number of nodes to add to target set when computing the protein-protein interaction network (STRING)
ppi_score_threshold	minimum score (0-1000) for retrieval of protein-protein interactions (STRING)
show_ppi	logical indicating if report should contain protein-protein interaction data (STRING)
show_drugs_in_ppi	logical indicating if targeted drugs (> phase 3) should be displayed in protein-protein interaction network (Open Targets Platform)
show_disease	logical indicating if report should contain disease associations (Open Targets Platform)
show_enrichment	logical indicating if report should contain functional enrichment/over-representation analysis (MSigDB, GO, KEGG, REACTOME etc.)
show_tcga_aberration	logical indicating if report should contain TCGA aberration plots (amplifications/deletions)
show_tcga_coexpression	logical indicating if report should contain TCGA co-expression data (RNAseq) of queryset with oncogenes/tumor suppressor genes
show_unknown_function	logical indicating if report should highlight target genes with unknown or poorly defined functions
show_prognostic_cancer_assoc	logical indicating if mRNA-based (single-gene) prognostic associations to cancer types should be listed
show_subcell_comp	logical indicating if report should list subcellular compartment annotations (ComPPI)
show_crispr_lof	logical indicating if report should list results from CRISPR/Cas9 loss-of-fitness screens (Project Score)
show_complex	logical indicating if report should list proteins in known protein complexes (CORUM)
show_tissue_cell	logical indicating if report should contain tissue-specificity and single cell-type specificity assessments of target genes, using data from the Human Protein Atlas

sigven/oncoEnrichR documentation built on April 9, 2021, 9:06 p.m.