API reference for Output() class

class autoclasswrapper.Output(root_in_name='autoclass', root_out_name='autoclass_out', tolerate_error=False)

AutoClass output files and results.

Parameters

• root_in_name (string, optional (default: "autoclass")) – Root name to read input files generated by autoclass. Example: “autoclass” will lead to “autoclass.db2”, “autoclass.model”, “autoclass.s-params”…

• root_out_name (string, optional (default: "autoclass_out")) – Root name to write output files Ex.: “autoclass_out” will lead to “autoclass_out.cdt”, “autoclass_out_stats.tsv”

• tolerate_error (bool, optional (default: False)) – If True, countinue generation of autoclass input files even if an error is encounter. If False, stop at first error.

had_error

Set to True if an error has been found in the generation of autoclass input files.

Type

bool (defaut False)

case_number

Number of cases (i.e. of genes/proteins).

Type

int (default 0)

class_number

Number of classes (i.e. clusters).

Type

int (default 0)

stats

Dataframe that contains, for all cases, main class and probability for all classes.

Type

Pandas dataframe (default None)

df

Dataframe that contains initial input data and associated clusters.

Type

Pandas dataframe (default None)

experiment_names

List of experiment (conditions) names. Corresponds to columns in the input data.

Type

list of string (defaut [])

aggregate_input_data(*args, **kwargs)

Aggregate autoclass classes with input data.

extract_results(*args, **kwargs)

Extract results from autoclass.

Results extracted are: - Number of cases (i.e. genes/proteins) - Number of classes (i.e. clusters) - For each case X, most probable class - For each case X, probability to belong to class Y

handle_error()

Handle error during data parsing and formating.

Function decorator.

Parameters

f (function) –

Returns

try_function

Return type

function wrapped into error handler

write_cdt(*args, **kwargs)

Write .cdt file for visualisation.

Parameters

with_proba (bool (default False), optional) – If True, also writes probability of case to belong to each class.

write_class_stats(*args, **kwargs)

Write class stat file.

Number of elements per class. Mean and standard deviation values per experiment. Missing values are skipped.

write_dendrogram(*args, **kwargs)

Write dendrogram of hierarchical clustering of classes to file.