HiC

class prody.chromatin.hic.HiC(title='Unknown', map=None, bin=None)

This class is used to store and preprocess Hi-C contact map. A GNM instance for analyzing the contact map can be also created by using this class.

calcGNM(n_modes=None, **kwargs)

Calculates GNM on the current Hi-C map. By default, n_modes is set to None and zeros to True.

getCompleteMap()

Obtains the complete contact map with unmapped regions.

getDomainList()

Returns a list of domain separations. The list has two columns: the first is for the domain starts and the second is for the domain ends.

getDomains()

Returns an 1D numpy.ndarray whose length is the number of loci. Each element is an index denotes to which domain the locus belongs.

getKirchhoff()

Builds a Kirchhoff matrix based on the contact map.

getTitle()

Returns title of the instance.

getTrimedMap()

Obtains the contact map without unmapped regions.

normalize(method=<function VCnorm>, **kwargs)

Applies chosen normalization on the current Hi-C map.

setDomains(labels, **kwargs)

Uses spectral clustering to identify structural domains on the chromosome.

Parameters:

• labels (ndarray, list) – domain labels

• method (func) – Label assignment algorithm used after Laplacian embedding.

setTitle(title)

Sets title of the instance.

view(spec='p', **kwargs)

Visualization of the Hi-C map and domains (if present). The function makes use of showMatrix().

Parameters:

• spec (str) – a string specifies how to preprocess the matrix. Blank for no preprocessing, ‘p’ for showing only data from p-th to 100-p-th percentile. ‘_’ is to suppress creating a new figure and paint to the current one instead. The letter specifications can be applied sequentially, e.g. ‘p_’.

• p (double) – specifies the percentile threshold.

prody.chromatin.hic.loadHiC(filename)

Returns HiC instance after loading it from file (filename). This function makes use of numpy.load() function. See also saveHiC().

prody.chromatin.hic.parseHiC(filename, **kwargs)

Returns an HiC from a Hi-C data file.

This function extends parseHiCStream().

Parameters:

filename (str) – the filename to the Hi-C data file.

prody.chromatin.hic.parseHiCStream(stream, **kwargs)

Returns an HiC from a stream of Hi-C data lines.

Parameters:

stream – Anything that implements the method read, seek (e.g. file, buffer, stdin)

prody.chromatin.hic.saveHiC(hic, filename=None, map=True, **kwargs)

Saves HiC model data as filename.hic.npz. If map is True, Hi-C contact map will not be saved and it can be loaded from raw data file later. If filename is None, name of the Hi-C instance will be used as the filename, after " " (white spaces) in the name are replaced with "_" (underscores). Upon successful completion of saving, filename is returned. This function makes use of numpy.savez() function.

prody.chromatin.hic.writeMap(filename, map, bin=None, format='%f')

Writes map to the file designated by filename.

Parameters:

• filename (str) – the file to be written.

• map (numpy.ndarray) – a Hi-C contact map.

• bin (int) – bin size of the map. If bin is None, map will be written in full matrix format.

• format (str) – output format for map elements.