Data Combination

combine_pymutations¶

Short description¶

Combines two PyMutation objects into a single instance, deduplicating variants, merging sample columns, and ensuring both input cohorts share the same genome assembly.

Signature¶

def combine_pymutations(pymut1: PyMutation, pymut2: PyMutation) -> PyMutation:

Parameters¶

Parameter	Type	Required	Description
`pymut1`	`PyMutation`	Yes	First mutation cohort. Its assembly must match that of `pymut2`.
`pymut2`	`PyMutation`	Yes	Second mutation cohort to merge with `pymut1`. Samples and annotations are integrated.

Return value¶

PyMutation – new object containing the union of variants, samples, and annotations from both inputs. Originals are left untouched.

Exceptions¶

ValueError: if pymut1 and pymut2 have different assembly values.

Minimal usage example¶

from pymutation import PyMutation
from pymutation.analysis import combine_pymutations

cohort_a = PyMutation.from_maf("tumours_setA.maf")
cohort_b = PyMutation.from_maf("tumours_setB.maf")

merged = combine_pymutations(cohort_a, cohort_b)
print(f"Merged cohort: {len(merged.samples)} samples, {len(merged.data)} variants")