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Get rank of genes according to association to cancer (Open Targets Platform)

Source: R/get_otp_rank.R
get_otp_rank.Rd

Downloads and returns a dataset that ranks genes according to aggregated association scores between genes and cancer phenotype terms from the Open Targets Platform

  • metadata - a data frame with metadata regarding annotation resources used

  • records - a data frame with gene scores/ranks (one record per gene and primary site)

Usage

get_otp_rank(cache_dir = NA, force_download = FALSE)

Arguments

cache_dir

Local directory for data download

force_download

Logical indicating if local cache should be overwritten (set to TRUE to re-download if file exists in cache)

Value

metadata - A data frame with 10 rows and 6 columns:

  • source - gene annotation source

  • annotation_data - type of annotations used

  • url - URL of annotation resource

  • citation - publication to cite for annotation source (citation; PMID)

  • version - version used

  • abbreviation - abbreviation used in column names of records

records - A data frame with 20,954 rows and 6 columns:

  • entrezgene - NCBI Entrez gene identifier

  • primary_site - Primary tumor site

  • tissue_assoc_score - tissue-specific aggregated association score

  • tissue_assoc_rank - tissue-specific cancer rank

  • global_assoc_score - pan-cancer aggregated association score

  • global_assoc_rank - cancer gene rank (pan-cancer, across tissues)

Examples

if (FALSE) { # \dontrun{
library(geneOncoX)
gene_otp_rank <- get_otp_rank(cache_dir = tempdir())
} # }