Package index • SCOUT

Google Sheets

Functions to read cohort tables from Google Sheets.

get_metadata(): Get SCOUT sample metadata
get_ground_truth_cna(): Get SCOUT ground truth CNA data
get_ground_truth_drivers(): Get SCOUT ground truth driver events
get_ground_truth_exposures(): Get SCOUT ground truth mutational signature exposures
get_sampling_information(): Get SCOUT sampling information
read_sheet(): Read a public Google Sheet and return a tibble

Zenodo — download

Functions to download and cache per-SPN archives from Zenodo.

get_ground_truth(): Get ground truth simulation data for a SCOUT SPN
get_sarek_results(): Get the local path to Sarek results for a SCOUT SPN
get_tumourevo_results(): Get the local path to tumourevo results for a SCOUT SPN
list_zenodo_files(): List files available in a Zenodo record

Ground truth getters

Access simulation ground truth data (mutations, CNA, forests).

get_mutations(): Get mutations from SCOUT ground truth
get_sample_names(): Get sample names for a SCOUT SPN
get_gender(): Get subject gender for a SCOUT SPN
get_tumour_type(): Get tumour type for a SCOUT SPN

Sarek getters

Access Sarek pipeline results (VCF and CNA files).

get_sarek_vcf(): Get Sarek VCF output files for a SCOUT SPN
get_sarek_cna(): Get Sarek CNA output files for a SCOUT SPN

tumourevo getters

Access tumourevo pipeline results by tool and analysis type.

get_tumourevo_driver(): Get tumourevo driver annotation paths
get_tumourevo_subclonal(): Get tumourevo subclonal deconvolution result paths
get_tumourevo_qc(): Get tumourevo QC result paths
get_tumourevo_signatures(): Get tumourevo signature deconvolution result paths