Create a new molpath_db object

Constructs a molpath_db object, which is a list of linked tibbles representing the core data model for molecular pathology workflows.

Usage

new_molpath_db(
  patients = tibble::tibble(patient_id = character(), age = integer(), sex = character(),
    diagnosis = character()),
  samples = tibble::tibble(sample_id = character(), patient_id = character(), sample_type
    = character(), date = as.Date(character()), source_file = character()),
  variants = tibble::tibble(sample_id = character(), gene = character(), variant =
    character(), classification = character(), vaf = double()),
  reports = tibble::tibble(sample_id = character(), report_type = character(),
    report_date = as.Date(character()), summary_text = character(), source_file =
    character()),
  clinical = tibble::tibble(patient_id = character(), parameter = character(), value =
    character(), date = as.Date(character()), source = character()),
  survival = tibble::tibble(patient_id = character(), os_months = double(), os_status =
    integer(), pfs_months = double(), pfs_status = integer()),
  metadata = list(creation_date = Sys.time(), source_files = character(), parser_versions
    = list())
)

Arguments

patients

A tibble with columns patient_id, age, sex, diagnosis, and optionally others.

samples

A tibble with columns sample_id, patient_id, sample_type, date, source_file, and optionally others.

variants

A tibble with columns sample_id, gene, variant, classification, vaf, and optionally others.

reports

A tibble with columns sample_id, report_type, report_date, summary_text, source_file, and optionally others.

clinical

A tibble with columns patient_id, parameter, value, date, source, and optionally others.

survival

A tibble with columns patient_id, os_months, os_status, pfs_months, pfs_status, and optionally others.

metadata

A list containing creation_date (POSIXct), source_files (character vector), and parser_versions (named list).

Value

An S3 object of class molpath_db.

Examples

db <- new_molpath_db()
db
#> 
#> ── molpath_db ──────────────────────────────────────────────────────────────────
#> ℹ patients: 0 records x 4 columns
#> ℹ samples: 0 records x 5 columns
#> ℹ variants: 0 records x 5 columns
#> ℹ reports: 0 records x 5 columns
#> ℹ clinical: 0 records x 5 columns
#> ℹ survival: 0 records x 5 columns
#> ℹ Created: "2026-04-17 17:35:49"
#> ℹ Source files: 0