Infer cDNA signal layout from pre- and post-tail region sizes

Independent visual cross-check of the orientation algorithm (detect_orientation_single). Compares the sizes of the pre-tail and post-tail regions of the raw signal; the larger side is assumed to be the transcript body. Per the empirical orientation finding, cDNA polyA reads carry the transcript body before the tail (body-first), while cDNA polyT reads carry it after (adapter-first).

Usage

infer_cdna_layout(
  poly_tail_start,
  poly_tail_end,
  signal_length,
  min_region_samples = 100L,
  strictness_ratio = 1.5
)

Arguments

poly_tail_start

Integer. 1-based start index of the poly tail in signal coordinates.

poly_tail_end

Integer. 1-based end index of the poly tail in signal coordinates.

signal_length

Integer. Total length of the raw signal vector.

min_region_samples

Integer. Minimum acceptable pre- or post-tail region size in samples. Defaults to 100.

strictness_ratio

Numeric. Required ratio of larger to smaller region for a non-ambiguous call. Defaults to 1.5.

Value

Character string: "polyA_layout" (body | tail | adapter), "polyT_layout" (adapter | tail | body), or "ambiguous".

Details

Returns "ambiguous" when either region is shorter than a minimum size guard, or when the larger / smaller ratio is below a strictness threshold. Both guards are deliberate - the function is intended as a strict secondary check, so borderline reads are flagged for manual review rather than silently committed to one orientation.

Used by launch_cdna_signal_browser to colour signal regions and surface algorithm-vs-layout disagreements.

See also

cdna_layout_agreement_marker, launch_cdna_signal_browser.