pastis.datasets.generate_dataset_from_distances¶

pastis.datasets.generate_dataset_from_distances(dis, alpha=- 3, beta=1, alpha_inter=None, lengths=None, distribution='NegativeBinomial', random_state=None, dispersion=7)¶

Generate dataset from distance matrix

Parameters

dis(n, n) ndarray

alpha : float, optional, default: -3

count-to-distance parameter

beta : float, optional, default: 1

coverage or scaling factor

alpha_interfloat, optional, default: None

count-to-distance parameter for inter-chromosomal count. When provided, lengths also needs to be provided

lengths : ndarray (L, ), optional, default: None

Vector of lengths of chromosomes.

distributionstring, optional, default: “NegativeBinomial”

The distribution used to draw contact counts from. Can be “Poisson”, “NB”, “NegativeBinomial”, or “Intensity”. If “Intensity” is provided, returns the intensity of the random process instead of a random distribution.

random_stateint, optional, default: None

Determines random number generation. Use an int to make the randomness deterministic.

dispersionfloat, optional, default: 7.

Dispersion parameter for the Negative Binomial distribution. Will be ignored for the Poisson distribution.

Returns

ndarray (n, n)

Examples using pastis.datasets.generate_dataset_from_distances¶

Generate a random dataset from a distance matrix¶