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

Description Usage Arguments

View source: R/onco_enrichr.R

Description

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

Usage

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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.