Package index • phewasFlow

Data and specifications

run_phewas(): Run one PheWAS testing family
run_phewas_contrast(): Compare nested PheWAS specifications on identical samples

plot_phewas_category_overlap(): Plot FDR signal overlap by phenotype group
plot_phewas_concordance(): Plot concordance between two PheWAS results
plot_phewas_effects(): Plot compatible native effects from a PheWAS comparison
plot_phewas_forest(): Draw a multi-run forest plot
plot_phewas_manhattan(): Plot a PheWAS Manhattan-style result
plot_phewas_volcano(): Plot a PheWAS volcano result
save_phewas_plot(): Save a PheWAS plot and optional audit sidecar

read_phewasflow_config(): Read a phewasFlow YAML configuration
validate_phewasflow_config(): Validate a phewasFlow configuration
config_to_phewas_spec(): Build a PheWAS specification from a configuration
create_phewas_manifest(): Create a deterministic shard manifest
run_phewas_shard(): Run one manifest shard
combine_phewas_shards(): Combine and globally correct completed PheWAS shards
write_phewas_bundle(): Write PheWAS results
read_phewas_bundle(): Read PheWAS results
phewasflow_cli(): Run the phewasFlow command-line interface