Package index • ukbflow

Authentication

Connect to the UK Biobank Research Analysis Platform (RAP) and manage project selection.

Explore and retrieve files from RAP project storage.

fetch_ls(): List files and folders at a remote RAP path
fetch_tree(): Print a remote RAP directory tree
fetch_url(): Get pre-authenticated download URL(s) for a remote RAP file or folder
fetch_file(): Download a file from RAP project storage
fetch_metadata(): Download the Showcase metadata folder
fetch_field(): Download the UKB field dictionary file

Extract UKB fields from the RAP dataset into R.

extract_ls(): List all approved fields in the UKB dataset
extract_pheno(): Extract phenotype data from a UKB dataset
extract_batch(): Submit a large-scale phenotype extraction job via table-exporter

Convert raw UKB column names and coded values to human-readable labels.

decode_names(): Rename UKB field ID columns to human-readable snake_case names
decode_values(): Decode UKB categorical column values using Showcase metadata

Build case definitions from HES, cancer registry, self-report, and First Occurrence data sources.

derive_selfreport(): Define a self-reported phenotype from UKB touchscreen data
derive_hes(): Derive a binary disease flag from UKB HES inpatient diagnoses
derive_cancer_registry(): Derive a binary disease flag from UKB cancer registry
derive_death_registry(): Derive a binary disease flag from UKB death registry
derive_first_occurrence(): Derive a binary disease flag from UKB First Occurrence fields
derive_icd10(): Derive a unified ICD-10 disease flag across multiple UKB data sources
derive_case(): Combine self-report and ICD-10 sources into a unified case definition

Derive continuous covariates, categorical cuts, follow-up time, and event timing variables.

derive_covariate(): Prepare UKB covariates for analysis
derive_cut(): Cut a continuous UKB variable into quantile-based or custom groups
derive_missing(): Handle informative missing labels in UKB decoded data
derive_age(): Compute age at event for one or more UKB outcomes
derive_followup(): Compute follow-up end date and follow-up time for survival analysis
derive_timing(): Classify disease timing relative to UKB baseline assessment

Submit, monitor, and retrieve results from RAP extraction jobs.

Fit regression models for UKB outcomes with automatic three-model adjustment framework.

assoc_coxph() assoc_cox(): Cox proportional hazards association analysis
assoc_logistic() assoc_logit(): Logistic regression association analysis
assoc_linear() assoc_lm(): Linear regression association analysis
assoc_coxph_zph() assoc_zph(): Proportional hazards assumption test for Cox regression
assoc_subgroup() assoc_sub(): Subgroup association analysis with optional interaction test
assoc_trend() assoc_tr(): Dose-response trend analysis
assoc_competing() assoc_fg(): Fine-Gray competing risks association analysis
assoc_lag(): Cox regression lag sensitivity analysis

End-to-end RAP-native pipeline for computing and validating polygenic risk scores with plink2.

grs_check(): Check and export a GRS weights file
grs_bgen2pgen(): Convert UKB imputed BGEN files to PGEN on RAP
grs_score(): Calculate genetic risk scores from PGEN files on RAP
grs_standardize() grs_zscore(): Standardise GRS columns by Z-score transformation
grs_validate(): Validate GRS predictive performance

Environment checks, synthetic data generation, missing-value summaries, pipeline snapshots, and cohort management.

ops_setup(): Check the ukbflow operating environment
ops_toy(): Generate toy UKB-like data for testing and development
ops_na(): Summarise missing values by column
ops_snapshot(): Record and review dataset pipeline snapshots
ops_snapshot_cols(): Retrieve column names recorded at a snapshot
ops_snapshot_diff(): Compare column names between two snapshots
ops_snapshot_remove(): Remove raw source columns recorded at a snapshot
ops_set_safe_cols(): Register additional safe columns protected from snapshot-based drops
ops_withdraw(): Exclude withdrawn participants from a dataset

Publication-quality forest plots and Table 1 for manuscripts.