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from SigProfilerAssignment import decomposition as decomp | ||
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def decompose_fit(samples, output, signatures=None, signature_database=None,nnls_add_penalty=0.05, nnls_remove_penalty=0.01, initial_remove_penalty=0.05,genome_build="GRCh37", cosmic_version=3.4, make_plots=True, collapse_to_SBS96=True,connected_sigs=True, verbose=False,devopts=None,new_signature_thresh_hold=0.8,exclude_signature_subgroups=None,exome=False,input_type='matrix',context_type="96",export_probabilities=True, export_probabilities_per_mutation=False): | ||
decomp.spa_analyze(samples=samples, output=output, signatures=signatures, signature_database=signature_database,nnls_add_penalty=nnls_add_penalty, nnls_remove_penalty=nnls_remove_penalty, initial_remove_penalty=initial_remove_penalty,genome_build=genome_build, cosmic_version=cosmic_version, make_plots=make_plots, collapse_to_SBS96=collapse_to_SBS96,connected_sigs=connected_sigs, verbose=verbose,decompose_fit_option= True,denovo_refit_option=False,cosmic_fit_option=False,devopts=devopts,new_signature_thresh_hold=new_signature_thresh_hold,exclude_signature_subgroups=exclude_signature_subgroups,exome=exome,input_type=input_type,context_type=context_type,export_probabilities=export_probabilities, export_probabilities_per_mutation=export_probabilities_per_mutation) | ||
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def denovo_fit(samples, output, signatures=None, signature_database=None,nnls_add_penalty=0.05,nnls_remove_penalty=0.01, initial_remove_penalty=0.05, genome_build="GRCh37", cosmic_version=3.4, make_plots=True, collapse_to_SBS96=True,connected_sigs=True, verbose=False,devopts=None,new_signature_thresh_hold=0.8,exome=False,input_type='matrix',context_type="96",export_probabilities=True, export_probabilities_per_mutation=False): | ||
decomp.spa_analyze(samples=samples, output=output, signatures=signatures, signature_database=signature_database,nnls_add_penalty=nnls_add_penalty, nnls_remove_penalty=nnls_remove_penalty, initial_remove_penalty=initial_remove_penalty,genome_build=genome_build, cosmic_version=cosmic_version, new_signature_thresh_hold=new_signature_thresh_hold, make_plots=make_plots, collapse_to_SBS96=collapse_to_SBS96,connected_sigs=connected_sigs, verbose=verbose,decompose_fit_option= False,denovo_refit_option=True,cosmic_fit_option=False,devopts=devopts,exome=exome,input_type=input_type,context_type=context_type,export_probabilities=export_probabilities, export_probabilities_per_mutation=export_probabilities_per_mutation) | ||
def decompose_fit( | ||
samples, | ||
output, | ||
signatures=None, | ||
signature_database=None, | ||
nnls_add_penalty=0.05, | ||
nnls_remove_penalty=0.01, | ||
initial_remove_penalty=0.05, | ||
genome_build="GRCh37", | ||
cosmic_version=3.4, | ||
make_plots=True, | ||
collapse_to_SBS96=True, | ||
connected_sigs=True, | ||
verbose=False, | ||
devopts=None, | ||
new_signature_thresh_hold=0.8, | ||
exclude_signature_subgroups=None, | ||
exome=False, | ||
input_type="matrix", | ||
context_type="96", | ||
export_probabilities=True, | ||
export_probabilities_per_mutation=False, | ||
): | ||
decomp.spa_analyze( | ||
samples=samples, | ||
output=output, | ||
signatures=signatures, | ||
signature_database=signature_database, | ||
nnls_add_penalty=nnls_add_penalty, | ||
nnls_remove_penalty=nnls_remove_penalty, | ||
initial_remove_penalty=initial_remove_penalty, | ||
genome_build=genome_build, | ||
cosmic_version=cosmic_version, | ||
make_plots=make_plots, | ||
collapse_to_SBS96=collapse_to_SBS96, | ||
connected_sigs=connected_sigs, | ||
verbose=verbose, | ||
decompose_fit_option=True, | ||
denovo_refit_option=False, | ||
cosmic_fit_option=False, | ||
devopts=devopts, | ||
new_signature_thresh_hold=new_signature_thresh_hold, | ||
exclude_signature_subgroups=exclude_signature_subgroups, | ||
exome=exome, | ||
input_type=input_type, | ||
context_type=context_type, | ||
export_probabilities=export_probabilities, | ||
export_probabilities_per_mutation=export_probabilities_per_mutation, | ||
) | ||
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def cosmic_fit(samples, output, signatures=None, signature_database=None,nnls_add_penalty=0.05, nnls_remove_penalty=0.01, initial_remove_penalty=0.05,genome_build="GRCh37", cosmic_version=3.4, make_plots=True, collapse_to_SBS96=True,connected_sigs=True, verbose=False,devopts=None,exclude_signature_subgroups=None,exome=False,input_type='matrix',context_type="96",export_probabilities=True, export_probabilities_per_mutation=False, sample_reconstruction_plots=False): | ||
decomp.spa_analyze(samples=samples, output=output, signatures=signatures, signature_database=signature_database,nnls_add_penalty=nnls_add_penalty, nnls_remove_penalty=nnls_remove_penalty, initial_remove_penalty=initial_remove_penalty,genome_build=genome_build, cosmic_version=cosmic_version, make_plots=make_plots, collapse_to_SBS96=collapse_to_SBS96,connected_sigs=connected_sigs, verbose=verbose,decompose_fit_option= False,denovo_refit_option=False,cosmic_fit_option=True,devopts=devopts,exclude_signature_subgroups=exclude_signature_subgroups,exome=exome,input_type=input_type,context_type=context_type,export_probabilities=export_probabilities, export_probabilities_per_mutation=export_probabilities_per_mutation, sample_reconstruction_plots=sample_reconstruction_plots) | ||
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def denovo_fit( | ||
samples, | ||
output, | ||
signatures=None, | ||
signature_database=None, | ||
nnls_add_penalty=0.05, | ||
nnls_remove_penalty=0.01, | ||
initial_remove_penalty=0.05, | ||
genome_build="GRCh37", | ||
cosmic_version=3.4, | ||
make_plots=True, | ||
collapse_to_SBS96=True, | ||
connected_sigs=True, | ||
verbose=False, | ||
devopts=None, | ||
new_signature_thresh_hold=0.8, | ||
exome=False, | ||
input_type="matrix", | ||
context_type="96", | ||
export_probabilities=True, | ||
export_probabilities_per_mutation=False, | ||
): | ||
decomp.spa_analyze( | ||
samples=samples, | ||
output=output, | ||
signatures=signatures, | ||
signature_database=signature_database, | ||
nnls_add_penalty=nnls_add_penalty, | ||
nnls_remove_penalty=nnls_remove_penalty, | ||
initial_remove_penalty=initial_remove_penalty, | ||
genome_build=genome_build, | ||
cosmic_version=cosmic_version, | ||
new_signature_thresh_hold=new_signature_thresh_hold, | ||
make_plots=make_plots, | ||
collapse_to_SBS96=collapse_to_SBS96, | ||
connected_sigs=connected_sigs, | ||
verbose=verbose, | ||
decompose_fit_option=False, | ||
denovo_refit_option=True, | ||
cosmic_fit_option=False, | ||
devopts=devopts, | ||
exome=exome, | ||
input_type=input_type, | ||
context_type=context_type, | ||
export_probabilities=export_probabilities, | ||
export_probabilities_per_mutation=export_probabilities_per_mutation, | ||
) | ||
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def cosmic_fit( | ||
samples, | ||
output, | ||
signatures=None, | ||
signature_database=None, | ||
nnls_add_penalty=0.05, | ||
nnls_remove_penalty=0.01, | ||
initial_remove_penalty=0.05, | ||
genome_build="GRCh37", | ||
cosmic_version=3.4, | ||
make_plots=True, | ||
collapse_to_SBS96=True, | ||
connected_sigs=True, | ||
verbose=False, | ||
devopts=None, | ||
exclude_signature_subgroups=None, | ||
exome=False, | ||
input_type="matrix", | ||
context_type="96", | ||
export_probabilities=True, | ||
export_probabilities_per_mutation=False, | ||
sample_reconstruction_plots=False, | ||
): | ||
decomp.spa_analyze( | ||
samples=samples, | ||
output=output, | ||
signatures=signatures, | ||
signature_database=signature_database, | ||
nnls_add_penalty=nnls_add_penalty, | ||
nnls_remove_penalty=nnls_remove_penalty, | ||
initial_remove_penalty=initial_remove_penalty, | ||
genome_build=genome_build, | ||
cosmic_version=cosmic_version, | ||
make_plots=make_plots, | ||
collapse_to_SBS96=collapse_to_SBS96, | ||
connected_sigs=connected_sigs, | ||
verbose=verbose, | ||
decompose_fit_option=False, | ||
denovo_refit_option=False, | ||
cosmic_fit_option=True, | ||
devopts=devopts, | ||
exclude_signature_subgroups=exclude_signature_subgroups, | ||
exome=exome, | ||
input_type=input_type, | ||
context_type=context_type, | ||
export_probabilities=export_probabilities, | ||
export_probabilities_per_mutation=export_probabilities_per_mutation, | ||
sample_reconstruction_plots=sample_reconstruction_plots, | ||
) |
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