get_x_data

improvelib.applications.drug_response_prediction.drp_utils.get_x_data(file, benchmark_dir, column_name, dtype=None)

Gets x data. Sets index to ID. Sets dtype if specified.

Used in preprocess.

Parameters:

filestr, Path

Name of x data file if in benchmark data, otherwise path to x data file.

benchmark_dirstr, Path

Path to benchmark data directory.

column_namestr

Name of ID column for x data.

dtypestr, optional

The dtype to enforce for this x data (default: None).

Returns:

datapd.DataFrame

DataFrame of x data (with dtype if specified), index set to ID.

Example

To load transcriptomics data:

omics = drp.get_x_data(file = params['cell_transcriptomic_file'],
                                    benchmark_dir = params['input_dir'],
                                    column_name = params['canc_col_name'])

To load mordred data:

drugs = drp.get_x_data(file = params['drug_mordred_file'],
                benchmark_dir = params['input_dir'],
                column_name = params['drug_col_name'])