Recompute M2 after subsetting¶

Problem¶

You have a fully processed splicing AnnData with valid M2 layers, and you want to subset it — for example, to keep only a specific cell type or to drop low-coverage events:

# Subset to a single cell type
adata_t = adata[adata.obs["cell_type"] == "T cell", :].copy()

# Or subset to highly variable events only
adata_hve = adata[:, adata.var["highly_variable"]].copy()

After subsetting the var axis (events), M2 is no longer valid. The old M2 values were computed with the full LJV group membership; removing some members from the group changes the correct M2 values for the remaining members.

print(adata_hve.uns["scsplice"]["m2_valid"])  # False — invalidated automatically

Solution¶

Call make_m2 on the subset:

import scsplice as scs

# Subset to HVE
adata_hve = adata[:, adata.var["highly_variable"]].copy()

# M2 was invalidated; recompute from the subset's group structure
scs.tl.make_m2(adata_hve, n_threads=4)

print(adata_hve.uns["scsplice"]["m2_valid"])  # True

M2 is now computed from the subset's var["group_id"], which reflects only the events still present.

Why subsetting cells does not require recomputation¶

Subsetting the obs axis (cells) does not change the LJV group structure — group_id is a property of the var axis, not the obs axis. M2 for the remaining cells is still the correct per-cell sum over each LJV group. The m2_valid flag remains True after a cell-only subset.

# Cell subsetting: M2 remains valid
adata_cells = adata[adata.obs["sample_id"] == "s1", :].copy()
print(adata_cells.uns["scsplice"]["m2_valid"])  # True — no recomputation needed

How `m2_valid` is managed¶

The m2_valid flag in adata.uns["scsplice"] is set to False by read_starsolo (M2 has not been computed yet) and by internal helpers whenever the var axis changes shape. It is set to True only by make_m2. Functions that require valid M2 — highly_variable_events and pseudo_correlation — check this flag and raise a ValueError if it is False.

Do not set m2_valid manually

Setting adata.uns["scsplice"]["m2_valid"] = True without recomputing M2 will cause incorrect results downstream. Always call make_m2 to revalidate.