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

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Documentation for package ‘ukbflow’ version 0.3.4

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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)