ClinicalData

class openomics.ClinicalData(file, patient_index, columns=None)

Bases: object

This class manages the clinical data tables to handle the patient’s phenotype data, as well as the treatment, and sample data associated to each patient.

Attributes Summary

pathologic_stage_map

Methods Summary

add_biospecimen_data([file_path, ...])	param file_path
add_drug_response_data([file_path, ...])	param file_path
build_clinical_samples(all_samples[, index])	Build table with samples clinical data from patients :param all_samples:
get_patient_barcodes()
get_sample_barcodes()
name()	Returns the name of the class, i.e. 'ClinicalData'.

Attributes Documentation

pathologic_stage_map = {'Stage IA': 'Stage I', 'Stage IB': 'Stage I', 'Stage IIA': 'Stage II', 'Stage IIB': 'Stage II', 'Stage IIIA': 'Stage III', 'Stage IIIB': 'Stage III'}

Methods Documentation

add_biospecimen_data(file_path='genome.wustl.edu_biospecimen_sample.txt', patient_col_name='bcr_patient_barcode', columns=['bcr_sample_barcode', 'sample_type'])

Parameters

• file_path –

• patient_col_name –

• columns –

add_drug_response_data(file_path='nationwidechildrens.org_clinical_drug.txt', patient_column='bcr_patient_barcode', columns=None, drug_name_col=None, response_column=None)

Parameters

• file_path –

• patient_column –

• columns –

• drug_name_col –

• response_column –

build_clinical_samples(all_samples, index='bcr_patient_barcode')

Build table with samples clinical data from patients :param all_samples:

Parameters

• all_samples –

• index –

get_patient_barcodes()

get_sample_barcodes()

classmethod name()

Returns the name of the class, i.e. ‘ClinicalData’