Load per-codeword transcript breakdowns for specific genes

Atera's per-transcript codeword_identity (which specific barcode/ codeword called each detection) is collapsed away by LoadAteraMolecules, which reports one combined position per gene. A gene can map to more than one distinct codeword (more than one probe/barcode design targeting the same gene); this instead returns one "<gene>_codeword_<id>" pseudo-feature per codeword, which is useful for a common QC question: whether different codewords for the same gene cluster differently in space (which would suggest a probe-specific artifact rather than true expression).

Usage

LoadAteraCodewords(object, data.dir, genes, fov = NULL)

Arguments

object: A Seurat object created by LoadAtera
data.dir: The same data.dir passed to the original LoadAtera call (the Atera output bundle directory)
genes: Character vector of one or more gene names to break down by codeword
fov: Name of the FOV to attach the resulting molecules to; defaults to the object's default FOV

Value

object, with one "<gene>_codeword_<id>" molecule entry per codeword mapping to each requested gene, merged into object[[fov]]'s existing molecule layer (regular genes loaded via LoadAteraMolecules are preserved, not overwritten; genes already broken down by a previous call are not re-fetched)