R

Table of Contents

• Installation
• Usage
• Functions

Installation

To install the latest release from CRAN:

install.packages("bedrockbio")

Usage

Load package:

library(bedrockbio)

List available namespaces and tables:

list_namespaces()
list_tables()

Lazily load a table (returns a tbl_lazy object):

pqtls_tbl_lazy <- load_table("ukb_ppp.pqtls")

Filter columns and rows of the lazy table using dplyr verbs:

library(dplyr)

pqtls_tbl_lazy <- pqtls_tbl_lazy |>
    filter(
        ancestry == "EUR",
        protein_id == "A0FGR8",
        neg_log_10_p_value >= 7.30  # p-value ~5e-8
    ) |>
    select(
        chromosome,
        position_grch38,
        effect_allele,
        other_allele,
        beta,
        neg_log_10_p_value
    )

Note

For best performance, filter rows and columns on the lazy tables before collecting into a tibble or data frame. This reduces the amount of data downloaded, which speeds up analysis and reduces memory pressure on the local machine.

It is particularly recommended to filter on the partitioning columns of a table. Use describe_table() or check a table’s documentation page to see the partitioning columns and their allowed values.

Collect to a tibble object (triggers data download):

pqtls_tbl <- pqtls_tbl_lazy |> collect()

Or, collect to a plain data frame (also triggers download):

pqtls_df <- pqtls_tbl_lazy |> as.data.frame()

Functions

Signature	Description	Returns
list_namespaces()	List namespace identifiers.	character
list_tables(namespace = NULL)	List all tables, filtered to a namespace if specified.	character
describe_namespace(name)	Inspect namespace metadata.	list
describe_table(name)	Inspect table metadata.	list
load_table(name)	Lazily load the specified table identifier.	tbl_lazy