PeakCaller#
- class PeakCaller(shape, num_peaks=1000, min_distance=1, min_boundary_distance=0, min_score=None, max_score=None, batch_dims=None, shm_handler=None, **kwargs)[source]#
Bases:
ABC
Base class for peak calling algorithms.
- Parameters:
- shapetuple of int
Score space shape. Used to determine dimension of peak calling problem.
- num_peaksint, optional
Number of candidate peaks to consider.
- min_distanceint, optional
Minimum distance between peaks, 1 by default
- min_boundary_distanceint, optional
Minimum distance to array boundaries, 0 by default.
- min_scorefloat, optional
Minimum score from which to consider peaks.
- max_scorefloat, optional
Maximum score upon which to consider peaks.
- batch_dimsint, optional
Peak calling batch dimensions.
- **kwargs
Optional keyword arguments.
- Raises:
- ValueError
If num_peaks is less than or equal to zero. If min_distances is less than zero.
Methods
PeakCaller.__call__
(scores, rotation_matrix, ...)Update the internal parameter store based on input array.
PeakCaller.call_peaks
(scores, **kwargs)Call peaks in the score space.
PeakCaller.merge
([candidates])Merge multiple instances of
PeakCaller
.PeakCaller.oversample_peaks
(scores, ...[, ...])Refines peaks positions in the corresponding score space.