Computes summary statistics across all layers of the database.
Value
An S3 object of class molpath_summary (a named list) containing
n_patients, n_samples, n_variants, n_reports, n_clinical,
diagnosis_distribution, variant_gene_counts, classification_distribution,
sample_type_distribution, date_range, and completeness.
Examples
db <- mp_example_db(n_patients = 20, seed = 1)
mp_summary(db)
#>
#> ── molpathR Database Summary ───────────────────────────────────────────────────
#>
#> ── Record counts ──
#>
#> • Patients: 20
#> • Samples: 36
#> • Variants: 2015
#> • Reports: 36
#> • Clinical: 85
#>
#> ── Diagnoses ──
#>
#> • Breast carcinoma: 4
#> • Colorectal carcinoma: 3
#> • Lung adenocarcinoma: 8
#> • Melanoma: 5
#>
#> ── Top mutated genes ──
#>
#> • TP53: 275
#> • BRAF: 169
#> • EGFR: 161
#> • KRAS: 157
#> • PIK3CA: 136
#> • ERBB2: 97
#> • NRAS: 94
#> • CDKN2A: 92
#> • PTEN: 91
#> • STK11: 91
#>
#> ── Completeness ──
#>
#> • patients_with_samples: 100%
#> • patients_with_variants: 100%
#> • patients_with_survival: 100%
#> • patients_with_clinical: 100%