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MsStratification: hypermutant stratification decision

Source: R/stratify.R
MsStratification.Rd

The decision record produced by [ms_stratify_hypermutants()]: the GMM cutoff in mutations per sample, the per-sample totals, the hypermutant / non-hypermutant sample lists and counts, the cutoff diagnostics, and the pipeline policy this decision feeds. Violations raise `msuiter_error_stratify`.

Usage

MsStratification(
  cutoff = integer(0),
  totals = integer(0),
  hyper = character(0),
  nonhyper = character(0),
  n_hyper = integer(0),
  n_nonhyper = integer(0),
  gmm = list(),
  policy = character(0),
  seed = integer(0)
)

Arguments

cutoff

single whole number: the cutoff (mutations per sample).

totals

named numeric vector of per-sample mutation totals.

hyper

character vector: sample ids with `total > cutoff` (the samples M2 excludes from de novo extraction).

nonhyper

character vector: the remaining sample ids (the de novo extraction input).

n_hyper, n_nonhyper

single whole numbers: group sizes.

gmm

named list of cutoff diagnostics: `retained_mean`, `retained_sd`, `retained_n`, `n_fits`, `converged` (feeds the load-distribution / cutoff plot).

policy

single string: the downstream pipeline semantics this decision feeds (`"exclude_de_novo_then_refit"`; upstream rescales instead – declared divergence, memo section 1.4).

seed

single whole number: the seed behind the GMM initialization.