Package index • SCOUT

Tables

Functions to read cohort annotation tables.

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
get_sample_names(): Get sample names for a SCOUT SPN
get_tumour_type(): Get tumour type for a SCOUT SPN
get_gender(): Get subject gender for a SCOUT SPN
read_sheet(): Read a public Google Sheet and return a tibble

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

get_sequencing_data(): Download SCOUT sequencing ground truth for a SPN
get_normal_data(): Download SCOUT normal sarek results for a 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

Access sequencing ground truth mutation data.

Access Sarek pipeline results. VCF callers: mutect2, strelka, freebayes, haplotypecaller. CNA callers: ascat, battenberg, sequenza, cnvkit.

Access tumourevo pipeline results by tool and analysis type.

get_tumourevo_snv(): Get tumourevo formatted SNV (vcf2cnaqc) file paths
get_tumourevo_cna(): Get tumourevo formatted CNA (cna2cnaqc) file paths
get_tumourevo_joint_table(): Get tumourevo joint CNAqc table (cnaqc2tsv)
get_tumourevo_vep(): Get tumourevo VEP annotated VCF file paths
get_tumourevo_driver(): Get tumourevo driver annotation file 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