cancer_association_rank: Rank a gene list according to cancer relevance to a tumor...

In sigven/oncoEnrichR: Cancer-dedicated gene set interpretation

Rank a gene list according to cancer relevance to a tumor type/site

Description

Function that ranks a list of human gene identifiers with respect to strength of association to a particular tumor type/site. Underlying association evidence for the cancer rank per site is pulled from the Open Targets Platform, see more details here.

Usage

cancer_association_rank(
  query = NULL,
  tumor_site = "Breast",
  query_id_type = "symbol",
  ignore_id_err = TRUE,
  include_gene_summary = FALSE,
  oeDB = NULL
)

Arguments

query	character vector with gene/query identifiers (minimum 1, maximum 2,500)
tumor_site	character indicating primary tumor site of interest
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
include_gene_summary	logical indicating if gene summary (NCBI/UniProt) should be included in output data tables
oeDB	oncoEnrichR data repository object - as returned from load_db()

Value

A list with two data frames: query genes ranked according to cancer relevance for the specified tumor site, and unranked query genes (no evidence found)

sigven/oncoEnrichR documentation built on March 5, 2025, 7:49 p.m.