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

Source: R/disease_drug.R
cancer_association_rank.Rd

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

oeDB

oncoEnrichR data repository object - as returned from load_db()

incude_gene_summary

logical indicating if gene summary (NCBI/UniProt) should be included in output data tables

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)