Resolve a cell-level merge specification into flat bin indices

Source: R/synth.R

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)”).

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.

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.

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.

Examples

if (FALSE) { # \dontrun{
# 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
)
} # }