Get Lazy DuckDB Table for CoMMpass Data

Returns a lazy `dplyr::tbl()` backed by DuckDB, reading from parquet files. The connection is managed by the caller and must be disconnected when done.

Usage

get_commpass_tbl(
  data_type = c("clinical", "biospecimen", "rnaseq_counts", "rnaseq_sample_metadata",
    "rnaseq_gene_metadata"),
  data_dir = "data/raw",
  con = NULL
)

Arguments

data_type

One of "clinical", "biospecimen", "rnaseq_counts", "rnaseq_sample_metadata", "rnaseq_gene_metadata"

data_dir

Base directory containing parquet files

con

An existing DuckDB connection. If NULL, a new in-memory connection is created and returned as an attribute of the result.

Value

A lazy dbplyr tbl. If con was NULL, the DuckDB connection is stored as attr(result, "connection") - caller must disconnect it.

See also

Other storage: query_commpass_parquet()

Examples

if (FALSE) { # \dontrun{
# Create connection and query
con <- DBI::dbConnect(duckdb::duckdb())
clinical_tbl <- get_commpass_tbl("clinical", con = con)

# Chain dplyr operations (lazy - not executed until collect)
result <- clinical_tbl |>
  dplyr::filter(gender == "female") |>
  dplyr::select(submitter_id, age_at_diagnosis, vital_status) |>
  dplyr::collect()

# Clean up
DBI::dbDisconnect(con, shutdown = TRUE)
} # }