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Filter by LIS score and VAF threshold (Wang et al., 2025, Genome Biology)

Source: R/filter2.R
filter_redeemR_by_LIS.Rd

Keeps variants with VAF (hetero) ≥ hetero_cutoff and LIS > lis_cutoff, enforces a minimum number of cells per variant, updates @GTsummary.filtered and @V.fitered, then rebuilds matrices and depth matrix.

Usage

filter_redeemR_by_LIS(
  redeemR_obj,
  lis_cutoff = 0.6,
  hetero_cutoff = 0.05,
  min_cells_per_variant = 2,
  QualifiedTotalCts = NULL,
  filter_name = NULL
)

Arguments

redeemR_obj

A redeemR object.

lis_cutoff

Numeric LIS threshold (default 0.6). LIS ≈ mean(hetero) / var(hetero).

hetero_cutoff

Numeric VAF (hetero) threshold (default 0.05).

min_cells_per_variant

Integer; minimum rows per variant (default 2).

QualifiedTotalCts

Optional “QualifiedTotalCts” table for depth rebuilding.

filter_name

Optional label passed to print_redeemR_matrix_dims.

Value

The updated redeemR object.