Launch the cDNA orientation validation browser

Minimum-useful companion to launch_signal_browser specifically for verifying cDNA orientation classifications against the raw signal layout. Shows one signal at a time with the algorithm's tail_type call, an independent size-ratio-inferred layout (see infer_cdna_layout), and an agreement marker so disagreements stand out visually.

Usage

launch_cdna_signal_browser(dorado_summary, pod5_dir, orientation_data, ...)

Arguments

dorado_summary

Character string or data frame. Path to a Dorado summary file or a data frame with at least read_id, filename, poly_tail_start, poly_tail_end columns. The Dorado >=1.4.0 input_filename alias is also accepted.

pod5_dir

Character string. Path to the directory containing POD5 files for the run.

orientation_data

Character string or data frame. Path to a TSV produced by detect_orientation_multiple, or that function's in-memory return value. Must contain read_id and tail_type; reference and sequence are used if present.

...

Additional arguments passed to runApp.

Value

Launches a Shiny application (does not return a value).

Details

Intended as a validation tool while check_tails_dorado_cDNA is still under construction; will be superseded by a fuller cDNA dashboard once cDNA-native CNN submodels are in place.

See also

launch_signal_browser, detect_orientation_multiple, infer_cdna_layout, cdna_layout_agreement_marker.

Examples

if (FALSE) { # \dontrun{
# Using files on disk
ninetails::launch_cdna_signal_browser(
  dorado_summary = "/path/to/dorado_summary.txt",
  pod5_dir = "/path/to/pod5/",
  orientation_data = "/path/to/sequence_with_tail_type.tsv"
)

# Using an in-memory orientation tibble (e.g. straight out of the pipeline)
classified <- ninetails::detect_orientation_multiple(
  sequence_files = my_seq_files, num_cores = 4
)
ninetails::launch_cdna_signal_browser(
  dorado_summary = "/path/to/dorado_summary.txt",
  pod5_dir = "/path/to/pod5/",
  orientation_data = classified
)
} # }