gunz_cm.metrics.ren.third_parties package

Subpackages

• gunz_cm.metrics.ren.third_parties.hicrep package
  • Submodules
  • gunz_cm.metrics.ren.third_parties.hicrep.hicrep module
    • hicrepSCC()
    • sccByDiag()
    • sccOfDiag()
  • gunz_cm.metrics.ren.third_parties.hicrep.utils module
    • cool2pixels()
    • coolerInfo()
    • getSubCoo()
    • meanFilterSparse()
    • pixels2Coo()
    • readMcool()
    • resample()
    • trimDiags()
    • upperDiagCsr()
    • varVstran()
  • Module contents
    • main()

Submodules

gunz_cm.metrics.ren.third_parties.hic_spector module

Module.

Examples

gunz_cm.metrics.ren.third_parties.hic_spector.Parse_matrix(file1, file2)

Function Parse_matrix.

Examples

Notes

gunz_cm.metrics.ren.third_parties.hic_spector.Parse_matrix_hic(file1, file2, chrn, resolution)

Function Parse_matrix_hic.

Examples

Notes

gunz_cm.metrics.ren.third_parties.hic_spector.Parse_matrix_lieberman(file1, file2, resolution)

Function Parse_matrix_lieberman.

Examples

Notes

gunz_cm.metrics.ren.third_parties.hic_spector.evec_distance(v1, v2)

Function evec_distance.

Examples

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gunz_cm.metrics.ren.third_parties.hic_spector.get_Laplacian(M)

Function get_Laplacian.

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gunz_cm.metrics.ren.third_parties.hic_spector.get_ipr(evec)

Function get_ipr.

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gunz_cm.metrics.ren.third_parties.hic_spector.get_reproducibility(M1, M2, num_evec=20, ipr_cut=5)

Function get_reproducibility.

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gunz_cm.metrics.ren.third_parties.hic_spector.main()

Function main.

Examples

Notes

gunz_cm.metrics.ren.third_parties.hic_spector_ahmed module

Module.

Examples

gunz_cm.metrics.ren.third_parties.hic_spector_ahmed.evec_distance(v1, v2)

Function evec_distance.

Examples

Notes

gunz_cm.metrics.ren.third_parties.hic_spector_ahmed.get_Laplacian(M)

Function get_Laplacian.

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Notes

gunz_cm.metrics.ren.third_parties.hic_spector_ahmed.get_hic_spector_test(M1, M2)

Function get_hic_spector_test.

Examples

Notes

gunz_cm.metrics.ren.third_parties.hic_spector_ahmed.get_hic_spector_train(M1, M2)

Function get_hic_spector_train.

Examples

Notes

gunz_cm.metrics.ren.third_parties.hic_spector_ahmed.get_ipr(evec)

Function get_ipr.

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gunz_cm.metrics.ren.third_parties.hic_spector_ahmed.get_score(M1, M2, num_evec)

Function get_score.

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Notes

gunz_cm.metrics.ren.third_parties.hic_spector_wrapper module

Module.

Examples

gunz_cm.metrics.ren.third_parties.hic_spector_wrapper.comp_hic_spector_third_party(cm1: lil_matrix, cm2: lil_matrix, num_evec: int = 20, ipr_cut: int = 5) → float

Compute the reproducibility score between two Hi-C matrices.

cm1sparse.lil_matrix

The first contact matrix.

cm2sparse.lil_matrix

The second contact matrix.

num_evecint, optional

The number of eigenvectors to use for the reproducibility score. Defaults to 20.

ipr_cutint, optional

The IPR cut-off value. Defaults to 5.

float

The reproducibility score between the two contact matrices.

This function checks if the input matrices are sparse and have integer data type. It then converts the matrices to COO format if necessary and computes the reproducibility score.

• Yeremia G. Adhisantoso (adhisant@tnt.uni-hannover.de)

• Llama3.1 8B - 8.0bpw

Examples

gunz_cm.metrics.ren.third_parties.hicrep_wrapper module

Wrapper for the third-party HiCRep implementation.

Examples

gunz_cm.metrics.ren.third_parties.hicrep_wrapper.comp_hicrep_third_party(cm1_coo: coo_matrix, cm2_coo: coo_matrix, max_k: int | None = None, max_dist_in_bp: int | None = None, resolution: int | None = None, downsample: bool = False, half_win_size: int | None = None, ena_common_region: bool = True, common_region_op: str = 'union', ena_reshaping: bool = True, remove_main_diag: bool = True) → float

Compute the similarity score between two contact matrices using Hi-CRep.

This function serves as a wrapper around a third-party implementation of the HiCRep algorithm.

cm1_coosp.coo_matrix

The first contact matrix in COO format.

cm2_coosp.coo_matrix

The second contact matrix in COO format.

max_kint, optional

The maximum distance in bins. Defaults to None.

max_dist_in_bpint, optional

The maximum distance in base pairs. Defaults to None.

resolutionint, optional

The resolution of the contact matrices. Defaults to None.

downsamplebool, optional

Whether to downsample the contact matrices. Defaults to False.

half_win_sizeint, optional

The half window size for mean filtering. Defaults to None.

ena_common_regionbool, optional

Whether to enable common region filtering. Defaults to True.

common_region_opstr, optional

The operation for common region filtering. Defaults to “union”.

ena_reshapingbool, optional

Whether to enable reshaping to enforce square shape. Defaults to True.

remove_main_diagbool, optional

Whether to remove the main diagonal. Defaults to True.

float

The similarity score between the two contact matrices.

Examples

Module contents