SnHiCPseudoBulk


class chr3d.SnHiCPseudoBulk(
    threads: int = 1,
)

Aggregate per-cell .cool matrices into a single pseudobulk matrix.

Merges all passing-QC cell matrices into one combined contact matrix suitable for comparison with bulk Hi-C data.

Parameters

Parameter	Type	Description
threads	`int`	Number of threads for cooler operations (default: 1)

Methods

aggregate


def aggregate(
    self,
    cell_cool_files: List[str],
    output_cool: str,
    output_mcool: str,
    resolutions: Optional[List[int]] = None,
) -> Dict[str, Any]

Merge per-cell .cool files into a pseudobulk matrix.

Parameters:

Parameter	Type	Description
cell_cool_files	`List[str]`	List of paths to per-cell `.cool` files
output_cool	`str`	Path for aggregated output `.cool` file
output_mcool	`str`	Path for multi-resolution `.mcool` file
resolutions	`Optional[List[int]]`	List of resolutions for zoomify (default: standard set)

Returns:

Dict[str, Any] with aggregation statistics.

aggregate is not yet fully implemented and will raise NotImplementedError.