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Get curated cancer biomarker datasets

Source: R/pharm_oncox.R
get_biomarkers.Rd

Downloads preprocessed datasets to a local cache directory and returns a curated set of genomic biomarkers from multiple sources (CIViC, CGI, MitelmanDB)

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

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

  • data - a list with four elements ('civic','cgi','mitelmandb','custom_fusions')

  • fpath - path to cache file

Usage

get_biomarkers(cache_dir = NA, force_download = F)

Arguments

cache_dir

Local directory for data download

force_download

Logical indicating if local cache should force downloaded (i.e. set to TRUE to re-download even if data exists in cache)

Value

Each entry of the source-specific (e.g. 'civic') entry in the data list contains a list of three data frames:

  • variant - list of all biomarker variants, extensively populated according to variant aliases (identifer - column variant_id)

  • clinical - cross-references between variants recorded in the variant data frame and clinical evidence items (identifier - column evidence_id) and underlying literature evidence (identifier - column source_id)

  • literature - lists literature for all source_id's listed in the clinical data frame