# Streamlined Workflow for UK Biobank Data Extraction, Analysis, and Visualization

## Documentation for package ‘ukbflow’ version 0.3.4

- DESCRIPTION file
- User guides, package vignettes and other documentation
- Package NEWS
- Package README

## Help Pages

assoc_competing | Fine-Gray competing risks association analysis
assoc_cox | Cox proportional hazards association analysis
assoc_coxph | Cox proportional hazards association analysis
assoc_coxph_zph | Proportional hazards assumption test for Cox regression
assoc_fg | Fine-Gray competing risks association analysis
assoc_lag | Cox regression lag sensitivity analysis
assoc_linear | Linear regression association analysis
assoc_lm | Linear regression association analysis
assoc_logistic | Logistic regression association analysis
assoc_logit | Logistic regression association analysis
assoc_sub | Subgroup association analysis with optional interaction test
assoc_subgroup | Subgroup association analysis with optional interaction test
assoc_tr | Dose-response trend analysis
assoc_trend | Dose-response trend analysis
assoc_zph | Proportional hazards assumption test for Cox regression
auth_list_projects | List available DNAnexus projects
auth_login | Login to DNAnexus with a token
auth_logout | Logout from DNAnexus
auth_select_project | Select a DNAnexus project
auth_status | Check current DNAnexus authentication status
decode_names | Rename UKB field ID columns to human-readable snake_case names
decode_values | Decode UKB categorical column values using Showcase metadata
derive_age | Compute age at event for one or more UKB outcomes
derive_cancer_registry | Derive a binary disease flag from UKB cancer registry
derive_case | Combine self-report and ICD-10 sources into a unified case definition
derive_covariate | Prepare UKB covariates for analysis
derive_cut | Cut a continuous UKB variable into quantile-based or custom groups
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_followup | Compute follow-up end date and follow-up time for survival analysis
derive_hes | Derive a binary disease flag from UKB HES inpatient diagnoses
derive_icd10 | Derive a unified ICD-10 disease flag across multiple UKB data sources
derive_missing | Handle informative missing labels in UKB decoded data
derive_selfreport | Define a self-reported phenotype from UKB touchscreen data
derive_timing | Classify disease timing relative to UKB baseline assessment
extract_batch | Submit a large-scale phenotype extraction job via table-exporter
extract_ls | List all approved fields in the UKB dataset
extract_pheno | Extract phenotype data from a UKB dataset
fetch_field | Download the UKB field dictionary file
fetch_file | Download a file from RAP project storage
fetch_ls | List files and folders at a remote RAP path
fetch_metadata | Download the Showcase metadata folder
fetch_tree | Print a remote RAP directory tree
fetch_url | Get pre-authenticated download URL(s) for a remote RAP file or folder
grs_bgen2pgen | Convert UKB imputed BGEN files to PGEN on RAP
grs_check | Check and export a GRS weights file
grs_score | Calculate genetic risk scores from PGEN files on RAP
grs_standardize | Standardise GRS columns by Z-score transformation
grs_validate | Validate GRS predictive performance
grs_zscore | Standardise GRS columns by Z-score transformation
job_ls | List recent DNAnexus jobs in the current project
job_path | Get the RAP file path of a completed DNAnexus job output
job_result | Load the result of a completed DNAnexus job into R
job_status | Check the current state of a DNAnexus job
job_wait | Wait for a DNAnexus job to finish
ops_na | Summarise missing values by column
ops_setup | Check the ukbflow operating environment
ops_set_safe_cols | Register additional safe columns protected from snapshot-based drops
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_toy | Generate toy UKB-like data for testing and development
ops_withdraw | Exclude withdrawn participants from a dataset
plot_forest | Publication-ready forest plot
plot_tableone | Publication-ready Table 1 (Baseline Characteristics)