gsynth.cell_merge: Resolve a cell-level merge specification into flat bin...

In misha: Toolkit for Analysis of Genomic Data

Resolve a cell-level merge specification into flat bin indices

Description

Unlike gsynth.bin_map, which merges bins independently along each dimension, gsynth.cell_merge resolves per-joint-cell redirects: each entry redirects one specific training cell (identified by its per-dimension values) to another specific training cell. This lets callers redirect arbitrary cells whose Cartesian position cannot be expressed via per-axis merges (e.g., “cell (GC=0.725, CG=0.05) –> cell (GC=0.70, CG=0.08)”).

Usage

gsynth.cell_merge(model, cell_merge, bin_merge = NULL)

Arguments

model	A gsynth.model object from gsynth.train.
cell_merge	A list of redirect specifications. Each entry is a named list with: from Numeric vector of length n_dims; one representative value per dimension that identifies the source cell. to Numeric vector of length n_dims; one representative value per dimension that identifies the target cell. A single data frame with columns from_1, from_2, ..., to_1, to_2, ... is also accepted and converted internally.
bin_merge	Optional sampling-time bin merge specification (same format as in gsynth.sample). When supplied, source and target per-dimension bin indices are remapped through the resulting per-axis maps before being combined into flat indices, so that cell values reference post-bin_merge cells.

Details

This function is primarily a utility for inspecting / debugging what gsynth.sample will do when invoked with the cell_merge argument. It returns a data frame describing, for every entry, the resolved source and target cells in both per-dimension-bin and flat-bin space.

Value

A data frame with one row per cell_merge entry and columns:

• from_<d>, to_<d> for each dimension d: 1-based bin index after any bin_merge remapping.

• source_flat, target_flat: 1-based flat bin index into model$model_data$cdf.

See Also

gsynth.bin_map, gsynth.sample

Examples

## Not run: 
# Resolve a redirect table before handing it to gsynth.sample:
redirects <- list(
    list(from = c(0.725, 0.05), to = c(0.70, 0.08)),
    list(from = c(0.75, 0.06), to = c(0.70, 0.08))
)
resolved <- gsynth.cell_merge(model, redirects)
print(resolved)

gsynth.sample(model, "out.fa",
    output_format = "fasta",
    cell_merge = redirects
)

## End(Not run)

misha documentation built on Aug. 24, 2026, 5:14 p.m.