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Get human cancer predisposition genes

Source: R/get_predisposition.R
get_predisposition.Rd

Downloads and retrieves a pre-processed dataset of human cancer predisposition genes (CPGs). Genes deemed relevant for cancer predisposition have been collected from multiple resources:

The dataset comes as a list object, with two elements:

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

  • records - a list with records of cancer predisposing gene, one record per gene

Usage

get_predisposition(cache_dir = NA, force_download = FALSE)

Arguments

cache_dir

Local directory for data download

force_download

Logical indicating if local cache should be overwritten

Value

metadata - A data frame with 1 row 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 594 rows and 8 columns:

  • symbol - official gene symbol

  • entrezgene - Entrez gene identifier

  • gene_biotype - gene biotype

  • cpg_moi - mechanism of inheritance (AD, AR)

  • cpg_syndrome_cui - Concept unique identifiers (CUI, UMLS) - inherited cancer syndromes

  • cpg_cancer_cui - Concept unique identifiers (CUI, UMLS) - inherited cancer conditions

  • cpg_source - Sources supporting predisposition gene PANEL_APP, CGC, TCGA_PANCAN_2018, OTHER, ACMG_SF

  • cpg_phenotypes - associated cancer phenotypes

  • cpg_mod - mechanism of disease)

Details

NOTE: The dataset also contains genes recommended for reporting of incidental findings (ACMG_SF).

Examples

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