get_biomarkers: Get curated cancer biomarker datasets

In sigven/oncoPharmaDB: Molecularly targeted cancer drugs and biomarkers

Get curated cancer biomarker datasets

Description

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

sigven/oncoPharmaDB documentation built on Dec. 24, 2024, 9:46 p.m.