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Get cancer gene panel collections from PanelApp

Source: R/get_panels.R
get_panels.Rd

Downloads and returns a collection of >40 cancer gene panels from Genomics England PanelApp. The dataset comes as a list object, with two elements:

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

  • records - a data frame with genes found in each panel

Usage

get_panels(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 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 2,566 rows and 13 columns:

  • genome_build - human assembly build (grch37/grch38)

  • id - panel identifier (local)

  • entrezgene - Entrez gene identifier

  • gene_biotype - gene biotype

  • genename - Gene name

  • ensembl_gene_id - Ensembl gene identifier

  • gepa_moi - mechanism of inheritance (Genomics England PanelApp)

  • gepa_penetrance - penetrance (Genomics England PanelApp)

  • gepa_confidence_level - confidence level (Genomics England PanelApp)

  • gepa_panel_name - panel name (Genomics England PanelApp)

  • gepa_panel_id - panel identifier (Genomics England PanelApp)

  • gepa_panel_version - panel version (Genomics England PanelApp)

  • gepa_phenotype - associated cancer phenotypes (Genomics England PanelApp)

  • gepa_panel_url - panel URL (Genomics England PanelApp)

Details

NOTE: Gene panel records are provided per genome build (filter on column genome_build to get a build-specific set of panels)

Examples

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