Remove variants with low median depth and depth-corrected homoplasmy

Removes variants whose per‑variant median depth (from @V.fitered$median_depth) is below a threshold, and also removes depth‑corrected possible homoplasmy (CellNPCT > 0.75). After filtering, rebuilds matrices and the depth matrix.

Usage

clean_redeem_remove_low_median_depth(ob, min_median_depth = 5)

Arguments

ob

A redeemR object that already has median_depth and CellNPCT in @V.fitered (see add_median_depth_to_redeemR).

min_median_depth

Numeric. Minimum per‑variant median depth to keep (default: 5).

Value

The updated redeemR object with variants filtered and matrices rebuilt.

Examples

# ob <- add_median_depth_to_redeemR(ob)
# ob <- clean_redeem_remove_low_median_depth(ob, min_median_depth = 10)