NORDic NI module

NORDic.NORDic_NI.functions module

NORDic.NORDic_NI.functions.import_all_solutions(solution_fname, quiet=False)

Import all solutions which have been generated

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Parameters

solution_fnamePython character string

header of solution files

quietPython bool

[default=False] : prints out verbose

Returns

solutionsPandas DataFrame

rows/[genes] x columns/[solution IDs] containing regulatory functions for each gene in each solution

NORDic.NORDic_NI.functions.network_identification(file_folder, taxon_id, path_to_genes=None, disgenet_args=None, network_fname=None, string_args=None, experiments_fname=None, lincs_args=None, edge_args=None, sig_args=None, bonesis_args=None, weights=None, seed=0, njobs=1, force_experiments=True, accept_nonRNA=False, preserve_network_sign=True)

Generates or retrieves the optimal network model

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Parameters

file_folderPython character string

path to which files should be saved

taxon_idPython integer

NCBI Taxonomy ID for the considered species

path_to_genesPython character string or None

[default=None] : path to the file containing gene names (one per line)

disgenet_argsPython dictionary or None

[default=None] : arguments to the DisGeNET API (see test files)

network_fnamePython character string or None

[default=None] : path to the file containing the prior knowledge network (see test files)

string_argsPython dictionary or None

[default=None] : arguments to the STRING API (see test files)

experiments_fnamePython character string or None

[default=None] : path to the file containing the matrix of gene expression data (genes x samples) (see test files for format)

lincs_argsPython dictionary or None

[default=None] : arguments to the LINCS L1000 API (see test files)

edge_argsPython dictionary or None

[default=None] : arguments to the processing of edges (see test files)

sig_argsPython dictionary or None

[default=None] : arguments to the processing of signatures (see test files)

bonesis_argsPython dictionary or None

[default=None] : arguments to building constraints and generating solutions using BoneSIS (see test files)

weightsPython dictionary or None

[default=None] : weights to the optimal model selection procedure (see test files)

seedPython integer

[default=0] : random seed

njobsPython integer

[default=1] : number of parallel jobs

force_experimentsPython bool

[default=True] : if set to True, returns an error if no experimental profile associated with the genes is found

accept_nonRNAPython bool

[default=False] : if set to False, ignores gene names which cannot be converted to EntrezIDs or which are not present in LINCS L1000

Returns

solutionPython character string

optimal model selected by the procedure

NORDic.NORDic_NI.functions.select_optimal_model(sols, weights, file_folder)

NORDic.NORDic_NI.functions.solution2cytoscape(solution, fname)

Convert a solution into a Cytoscape-readable file

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Parameters

solutionPandas Series

rows/[genes]

fnamePython character string

path to Cytoscape-readable SIF and XML (style) files (no extension)

Returns

None

writes a Cytoscape-readable file

NORDic.NORDic_NI.functions.solution_generation(file_folder, taxon_id, path_to_genes=None, disgenet_args=None, network_fname=None, string_args=None, experiments_fname=None, lincs_args=None, edge_args=None, sig_args=None, bonesis_args=None, weights=None, seed=0, njobs=1, force_experiments=True, accept_nonRNA=False, preserve_network_sign=True)

Generates or retrieves the optimal network model

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Parameters

file_folderPython character string

path to which files should be saved

taxon_idPython integer

NCBI Taxonomy ID for the considered species

path_to_genesPython character string or None

path to the file containing gene names (one per line)

disgenet_argsPython dictionary or None

arguments to the DisGeNET API (see test files)

network_fnamePython character string or None

path to the file containing the prior knowledge network (see test files)

string_argsPython dictionary or None

arguments to the STRING API (see test files)

experiments_fnamePython character string or None

path to the file containing the matrix of gene expression data (genes x samples) (see test files for format)

lincs_argsPython dictionary or None

arguments to the LINCS L1000 API (see test files)

edge_argsPython dictionary or None

arguments to the processing of edges (see test files)

sig_argsPython dictionary or None

arguments to the processing of signatures (see test files)

bonesis_argsPython dictionary or None

arguments to building constraints and generating solutions using BoneSIS (see test files)

seedPython integer

[default=0] : random seed

njobsPython integer

[default=1] : number of parallel jobs

force_experimentsPython bool

[default=True] : if set to True, returns an error if no experimental profile associated with the genes is found

accept_nonRNAPython bool

[default=False] : if set to False, ignores gene names which cannot be converted to EntrezIDs or which are not present in LINCS L1000

Returns

solutionPython character string

optimal model selected by the procedure

NORDic.NORDic_NI.functions.visualize_models(sols, file_folder)

Selection of an optimal model in a set of solutions, based on a topology-based desirability function

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Parameters

solsPandas DataFrame

rows/[genes] x columns/[solution IDs]

weightsPython dictionary

weight for each graph characteristic

Returns

solutionPandas DataFrame

rows/[genes] x column/[solution ID] selected solution