PeakCaller

class PeakCaller(number_of_peaks=1000, min_distance=1, min_boundary_distance=0, batch_dims=None, minimum_score=None, maximum_score=None, **kwargs)

Bases: ABC

Base class for peak calling algorithms.

Parameters:

number_of_peaksint, optional

Number of candidate peaks to consider.

min_distanceint, optional

Minimum distance between peaks.

min_boundary_distanceint, optional

Minimum distance to array boundaries.

batch_dimsint, optional

Peak calling batch dimensions.

minimum_scorefloat

Minimum score from which to consider peaks. If provided, superseeds limits presented by PeakCaller.number_of_peaks.

maximum_scorefloat

Maximum score upon which to consider peaks,

**kwargs

Optional keyword arguments.

Raises:

ValueError

If number_of_peaks is less than or equal to zero. If min_distances is less than zero.

Methods

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.