Package index • biobouncer

Check identifiers

The core entry points. One returns a table, the other a logical vector.

check_id(): Check biological identifiers
is_valid_id(): Test biological identifiers

Clean a column

Validate and repair a whole column in one call.

report_id() summary(<biobouncer_report>) print(<biobouncer_report>): Validate and report on a column of identifiers
repair_id(): Repair a column of identifiers

Generate test data

Build a synthetic, labeled column of ids for any source.

synthesize_ids(): Generate a synthetic column of identifiers

What can be checked

List the source databases and read their metadata.

sources(): List available source databases
source_info(): Describe the available sources

Snapshots and cache

Manage the offline snapshots that back cache mode.

biobouncer_pull(): Download a snapshot for cache mode
biobouncer_snapshots(): List installed snapshots
biobouncer_cache_dir(): Snapshot cache directory

Validation framework adapters

Thin wrappers over the core classifier for checkmate, shinyvalidate, and assertr or validate.

assert_valid_id(): Assert that identifiers are valid
check_valid_id(): Check that identifiers are valid
test_valid_id(): Test whether identifiers are valid
sv_biobouncer(): Create a shinyvalidate rule
id_predicate(): Build a vectorized predicate for data-frame validation

Package

biobouncer biobouncer-package: biobouncer: Validate Biological Identifiers and Inputs