API

Installation

R

To install the latest release from CRAN:

# COMING SOON -- PACKAGE NOT YET ON CRAN
install.packages("bedrockbio");

Python

To install the latest release from PyPI:

pip install bedrock-bio

Usage

R

Load the package (and dplyr for downstream data frame manipulation):

library(bedrockbio)
library(dplyr)

List available datasets:

list_datasets()

Load a dataset:

# all partition fields for a dataset must be specified, see docs for dataset-specific partition columns
df <- load_dataset('ukb_ppp.pqtls', ancestry="EAS", protein_id="A0FGR8", panel="Neurology_II")

Manipulate with dplyr verbs:

df |>
    select(
        chromosome, 
        position, 
        effect_allele, 
        other_allele, 
        beta, 
        neg_log_10_p_value
    ) |>
    slice_max(
        neg_log_10_p_value, n=10
    ) |>
    mutate(
        p_value=10^(-neg_log_10_p_value)
    )

Python

Load the package (and polars for downstream data frame manipulation):

import bedrock_bio as bb
import polars as pl

List available datasets:

bb.list_datasets()

Load a dataset into a Polars DataFrame:

# all partition fields for a dataset must be specified, see docs for dataset-specific partition columns
df = bb.load_dataset('ukb_ppp.pqtls', ancestry='EUR', protein_id='A0FGR8', panel='Neurology_II').pl()

Manipulate with Polars methods:

df \
    .select(
        'chromosome', 
        'position', 
        'effect_allele', 
        'other_allele', 
        'beta', 
        'neg_log_10_p_value'
    ) \
    .top_k(
        10, by='neg_log_10_p_value'
    ) \
    .with_columns(
        10**-pl.col('neg_log_10_p_value')
    )