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Build a molpath_db from parsed data objects

Source: R/database.R
mp_build_db.Rd

Constructs a unified molpath_db database object from one or more molpath_parsed objects. Each parsed object is categorized by its source_type and merged into the appropriate database table.

Usage

mp_build_db(...)

Arguments

...

One or more molpath_parsed objects, or lists of molpath_parsed objects. All objects are flattened and processed.

Value

A molpath_db S3 object containing linked patients, samples, variants, reports, clinical, survival, and metadata tables.

Details

Source types map to database tables as follows:

  • "vcf", "fastq", "bam" – variants

  • "xml_report" – variants and reports

  • "pdf_report" – reports

  • "nexus_pathology" – patients and samples

  • "nexus_clinical" – clinical

  • "survival" – survival

Examples

# \donttest{
# Build from a molpath_parsed object
surv_parsed <- new_molpath_parsed(
  data = tibble::tibble(
    patient_id = c("P1", "P2"),
    os_months = c(12, 24),
    os_status = c(1L, 0L),
    pfs_months = c(6, 18),
    pfs_status = c(1L, 0L)
  ),
  source_type = "survival",
  source_file = "test.csv"
)
db <- mp_build_db(surv_parsed)
#> 
#> ── Building molpath database ──
#> 
#> ℹ Processing 1 parsed object.
#> ✔ Database built successfully.
#> ℹ Tables: 0 patients, 0 samples, 0 variants, 0 reports, 0 clinical records, 2 survival records.
# }