oktoberfest.data.Spectra

class oktoberfest.data.Spectra(*args, **kwargs)

Main to init spectra data.

Parameters:

Return type:

Any

__init__(*args, **kwargs)

Parameters:

Return type:

None

Methods

`add_column`(data[, name])	Add column to spectra data.
`add_intensities`(intensities, annotation, ...)	Add predicted intensities and convert to sparse matrix.
`add_intensities_without_mapping`(intensities, ...)	Add predicted intensities and convert to sparse matrix.
`add_list_of_predicted_intensities`(...)	Add chunks of predicted intensities and convert to sparse matrix.
`add_matrix_from_hdf5`(intensity_data, ...)	Concatenate intensity df as a sparse matrix to our data.
`add_mzs`(mzs, fragment_type)	Add mass to charge ratios.
`convert_to_df`()	Gives back spectra_data instance as a pandas Dataframe.
`filter_by_score`(threshold)	Filter out peptides with search engine score below threshold in-place.
`from_hdf5`(input_file)	Read from hdf5 file.
`get_matrix`(fragment_type)	Get intensities sparse matrix from AnnData object.
`get_meta_data`()	Get meta data with intensity, mz and intensity predictions as pd.DataFrame.
`preprocess_for_machine_learning`([...])	Filter and preprocess for machine learning applications and transform into a Parquet-serializable dataframe.
`remove_decoys`()	Remove decoys in-place.
`remove_duplicates`(num_duplicates)	Filter out (peptide, charge, collision energy) duplicates if there's more than n_duplicates.
`write_as_hdf5`(output_file)	Write spectra_data to hdf5 file.

Attributes