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Create a synthetic molecular pathology database

Source: R/example_data.R
mp_example_db.Rd

Generates a realistic but entirely synthetic molpath_db object containing patients, samples, variants, reports, clinical data, and survival data. The data set is designed to mirror the structure of a real-world molecular pathology database with plausible clinical correlations, including diagnosis-specific mutation profiles, TNM staging, and survival outcomes.

Usage

mp_example_db(n_patients = 150, seed = 42)

Arguments

n_patients

Integer. Number of patients to generate. Default 150.

seed

Integer. Random seed for reproducibility. Default 42.

Value

A molpath_db object (S3 list) containing:

patients

A tibble with columns patient_id, age, sex, diagnosis, diagnosis_date.

samples

A tibble with columns sample_id, patient_id, sample_type, date, source_file.

variants

A tibble with columns sample_id, gene, variant, variant_type, classification, vaf, chromosome, position, ref_allele, alt_allele.

reports

A tibble with columns sample_id, report_type, report_date, summary_text, source_file.

clinical

A tibble with columns patient_id, parameter, value, date, source.

survival

A tibble with columns patient_id, os_months, os_status, pfs_months, pfs_status.

Examples

db <- mp_example_db()
db$patients
#> # A tibble: 150 × 5
#>    patient_id      age sex   diagnosis            diagnosis_date
#>    <chr>         <int> <chr> <chr>                <date>        
#>  1 PAT-2024-0001    78 M     Colorectal carcinoma 2021-04-10    
#>  2 PAT-2024-0002    55 F     Lung adenocarcinoma  2023-10-17    
#>  3 PAT-2024-0003    66 F     Breast carcinoma     2022-08-26    
#>  4 PAT-2024-0004    69 F     Breast carcinoma     2024-05-20    
#>  5 PAT-2024-0005    66 M     Colorectal carcinoma 2022-05-19    
#>  6 PAT-2024-0006    60 M     Lung adenocarcinoma  2021-10-08    
#>  7 PAT-2024-0007    80 F     Lung adenocarcinoma  2022-06-20    
#>  8 PAT-2024-0008    60 M     Breast carcinoma     2022-06-12    
#>  9 PAT-2024-0009    85 M     Melanoma             2023-10-24    
#> 10 PAT-2024-0010    61 F     Breast carcinoma     2023-04-04    
#> # ℹ 140 more rows
nrow(db$variants)
#> [1] 2361

# Smaller data set for quick tests
db_small <- mp_example_db(n_patients = 20, seed = 123)