Discrete Copy Number Alterations#

The module discrete_copy_number_alterations provides functions related to Discrete Copy Number Alterations section of cBioPortal Web Public API.

pybioportal.discrete_copy_number_alterations.fetch_discrete_copy_numbers_in_molecular_profile(molecular_profile_id, entrez_gene_ids=None, sample_ids=None, sample_list_id=None, discrete_cn_evt_type='HOMDEL_AND_AMP', projection='SUMMARY')#

Fetch discrete copy number alterations in a molecular profile by sample list ID.

Parameters:

molecular_profile_id (str) – Molecular Profile ID (e.g., “brca_tcga_gistic”).
entrez_gene_ids (list of str) – List of Entrez Gene IDs (e.g., [“2023”, “4853”, “54940”]).
sample_ids (list of str) – List of Sample IDs (e.g., [“TCGA-AR-A1AR-01”, “TCGA-E2-A1BC-01”] and sample_list_id set to None).
sample_list_id (str) – Sample List ID (e.g., “acc_tcga_all” and sample_ids set to None).
discrete_cn_evt_type (str) –
Type of the copy number event.

Possible values:
- ”ALL”: All events.
- ”AMP”: Amplification.
- ”DIPLOID”: Diploid.
- ”GAIN”: Gain.
- ”HETLOSS”: Heterozygous loss.
- ”HOMDEL”: Homozygous deletion.
- ”HOMDEL_AND_AMP”: Homozygous deletion and amplification (default).
projection (str) –
Level of detail of the response.

Possible values:
- ”DETAILED”: Detailed information.
- ”ID”: Information with only IDs.
- ”META”: Metadata information.
- ”SUMMARY”: Summary information (default).

Returns:

A DataFrame containing discrete copy number alterations.

Return type:

pandas.DataFrame

pybioportal.discrete_copy_number_alterations.get_discrete_copy_numbers_in_molecular_profile(molecular_profile_id, sample_list_id, discrete_cn_evt_type='HOMDEL_AND_AMP', projection='SUMMARY')#

Get discrete copy number alterations in a molecular profile by sample list ID.

Parameters:

molecular_profile_id (str) – Molecular Profile ID (e.g., “acc_tcga_gistic”).
sample_list_id (str) – Sample List ID (e.g., “acc_tcga_all”).
discrete_cn_evt_type (str) –
Type of the copy number event.

Possible values:
- ”ALL”: All events.
- ”AMP”: Amplification.
- ”DIPLOID”: Diploid.
- ”GAIN”: Gain.
- ”HETLOSS”: Heterozygous loss.
- ”HOMDEL”: Homozygous deletion.
- ”HOMDEL_AND_AMP”: Homozygous deletion and amplification (default).
projection (str) –
Level of detail of the response.

Possible values:
- ”DETAILED”: Detailed information.
- ”ID”: Information with only IDs.
- ”META”: Metadata information.
- ”SUMMARY”: Summary information (default).

Returns:

A DataFrame containing discrete copy number alterations.

Return type:

pandas.DataFrame

Examples#

from pybioportal import discrete_copy_number_alterations as dcna

df1 = dcna.get_discrete_copy_numbers_in_molecular_profile(molecular_profile_id="brca_tcga_gistic",
                                                          sample_list_id="brca_tcga_all",
                                                          projection="SUMMARY")
df1

	uniqueSampleKey	uniquePatientKey	molecularProfileId	sampleId	patientId	entrezGeneId	studyId	alteration
0	VENHQS1BUi1BMUFSLTAxOmJyY2FfdGNnYQ	VENHQS1BUi1BMUFSOmJyY2FfdGNnYQ	brca_tcga_gistic	TCGA-AR-A1AR-01	TCGA-AR-A1AR	4853	brca_tcga	2
1	VENHQS1BUi1BMUFSLTAxOmJyY2FfdGNnYQ	VENHQS1BUi1BMUFSOmJyY2FfdGNnYQ	brca_tcga_gistic	TCGA-AR-A1AR-01	TCGA-AR-A1AR	51205	brca_tcga	2
2	VENHQS1BUi1BMUFSLTAxOmJyY2FfdGNnYQ	VENHQS1BUi1BMUFSOmJyY2FfdGNnYQ	brca_tcga_gistic	TCGA-AR-A1AR-01	TCGA-AR-A1AR	100874392	brca_tcga	2
3	VENHQS1BUi1BMUFSLTAxOmJyY2FfdGNnYQ	VENHQS1BUi1BMUFSOmJyY2FfdGNnYQ	brca_tcga_gistic	TCGA-AR-A1AR-01	TCGA-AR-A1AR	284615	brca_tcga	2
4	VENHQS1BUi1BMUFSLTAxOmJyY2FfdGNnYQ	VENHQS1BUi1BMUFSOmJyY2FfdGNnYQ	brca_tcga_gistic	TCGA-AR-A1AR-01	TCGA-AR-A1AR	148741	brca_tcga	2
...	...	...	...	...	...	...	...	...
613540	VENHQS1FMi1BMUJDLTAxOmJyY2FfdGNnYQ	VENHQS1FMi1BMUJDOmJyY2FfdGNnYQ	brca_tcga_gistic	TCGA-E2-A1BC-01	TCGA-E2-A1BC	57606	brca_tcga	-2
613541	VENHQS1FMi1BMUJDLTAxOmJyY2FfdGNnYQ	VENHQS1FMi1BMUJDOmJyY2FfdGNnYQ	brca_tcga_gistic	TCGA-E2-A1BC-01	TCGA-E2-A1BC	201780	brca_tcga	-2
613542	VENHQS1FMi1BMUJDLTAxOmJyY2FfdGNnYQ	VENHQS1FMi1BMUJDOmJyY2FfdGNnYQ	brca_tcga_gistic	TCGA-E2-A1BC-01	TCGA-E2-A1BC	7006	brca_tcga	-2
613543	VENHQS1FMi1BMUJDLTAxOmJyY2FfdGNnYQ	VENHQS1FMi1BMUJDOmJyY2FfdGNnYQ	brca_tcga_gistic	TCGA-E2-A1BC-01	TCGA-E2-A1BC	326340	brca_tcga	-2
613544	VENHQS1FMi1BMUJDLTAxOmJyY2FfdGNnYQ	VENHQS1FMi1BMUJDOmJyY2FfdGNnYQ	brca_tcga_gistic	TCGA-E2-A1BC-01	TCGA-E2-A1BC	9750	brca_tcga	-2

613545 rows × 8 columns

df2a = dcna.fetch_discrete_copy_numbers_in_molecular_profile(molecular_profile_id="brca_tcga_gistic",
                                                             entrez_gene_ids=[2023,4853,54940],
                                                             sample_ids=["TCGA-AR-A1AR-01", "TCGA-E2-A1BC-01"])
df2a

	uniqueSampleKey	uniquePatientKey	molecularProfileId	sampleId	patientId	entrezGeneId	studyId	alteration
0	VENHQS1BUi1BMUFSLTAxOmJyY2FfdGNnYQ	VENHQS1BUi1BMUFSOmJyY2FfdGNnYQ	brca_tcga_gistic	TCGA-AR-A1AR-01	TCGA-AR-A1AR	4853	brca_tcga	2
1	VENHQS1FMi1BMUJDLTAxOmJyY2FfdGNnYQ	VENHQS1FMi1BMUJDOmJyY2FfdGNnYQ	brca_tcga_gistic	TCGA-E2-A1BC-01	TCGA-E2-A1BC	54940	brca_tcga	-2

df2b = dcna.fetch_discrete_copy_numbers_in_molecular_profile(molecular_profile_id="brca_tcga_gistic",
                                                             entrez_gene_ids=[2023,4853,54940],
                                                             sample_list_id="brca_tcga_all")
df2b

	uniqueSampleKey	uniquePatientKey	molecularProfileId	sampleId	patientId	entrezGeneId	studyId	alteration
0	VENHQS1BQy1BMjNILTAxOmJyY2FfdGNnYQ	VENHQS1BQy1BMjNIOmJyY2FfdGNnYQ	brca_tcga_gistic	TCGA-AC-A23H-01	TCGA-AC-A23H	2023	brca_tcga	-2
1	VENHQS1HTS1BM1hMLTAxOmJyY2FfdGNnYQ	VENHQS1HTS1BM1hMOmJyY2FfdGNnYQ	brca_tcga_gistic	TCGA-GM-A3XL-01	TCGA-GM-A3XL	2023	brca_tcga	-2
2	VENHQS1BNy1BNFNFLTAxOmJyY2FfdGNnYQ	VENHQS1BNy1BNFNFOmJyY2FfdGNnYQ	brca_tcga_gistic	TCGA-A7-A4SE-01	TCGA-A7-A4SE	2023	brca_tcga	-2
3	VENHQS1PTC1BOTdDLTAxOmJyY2FfdGNnYQ	VENHQS1PTC1BOTdDOmJyY2FfdGNnYQ	brca_tcga_gistic	TCGA-OL-A97C-01	TCGA-OL-A97C	2023	brca_tcga	-2
4	VENHQS1BOC1BMDlYLTAxOmJyY2FfdGNnYQ	VENHQS1BOC1BMDlYOmJyY2FfdGNnYQ	brca_tcga_gistic	TCGA-A8-A09X-01	TCGA-A8-A09X	2023	brca_tcga	-2
...	...	...	...	...	...	...	...	...
168	VENHQS1BMi1BMDRULTAxOmJyY2FfdGNnYQ	VENHQS1BMi1BMDRUOmJyY2FfdGNnYQ	brca_tcga_gistic	TCGA-A2-A04T-01	TCGA-A2-A04T	54940	brca_tcga	2
169	VENHQS1BTy1BMEo0LTAxOmJyY2FfdGNnYQ	VENHQS1BTy1BMEo0OmJyY2FfdGNnYQ	brca_tcga_gistic	TCGA-AO-A0J4-01	TCGA-AO-A0J4	54940	brca_tcga	2
170	VENHQS1BUS1BMDRMLTAxOmJyY2FfdGNnYQ	VENHQS1BUS1BMDRMOmJyY2FfdGNnYQ	brca_tcga_gistic	TCGA-AQ-A04L-01	TCGA-AQ-A04L	54940	brca_tcga	2
171	VENHQS1BMi1BMDRVLTAxOmJyY2FfdGNnYQ	VENHQS1BMi1BMDRVOmJyY2FfdGNnYQ	brca_tcga_gistic	TCGA-A2-A04U-01	TCGA-A2-A04U	54940	brca_tcga	2
172	VENHQS1CSC1BMEJQLTAxOmJyY2FfdGNnYQ	VENHQS1CSC1BMEJQOmJyY2FfdGNnYQ	brca_tcga_gistic	TCGA-BH-A0BP-01	TCGA-BH-A0BP	54940	brca_tcga	2

173 rows × 8 columns

df2c = dcna.fetch_discrete_copy_numbers_in_molecular_profile(molecular_profile_id="brca_tcga_gistic",
                                                             sample_list_id="brca_tcga_all")
df2c

	uniqueSampleKey	uniquePatientKey	molecularProfileId	sampleId	patientId	entrezGeneId	studyId	alteration
0	VENHQS1BUi1BMUFSLTAxOmJyY2FfdGNnYQ	VENHQS1BUi1BMUFSOmJyY2FfdGNnYQ	brca_tcga_gistic	TCGA-AR-A1AR-01	TCGA-AR-A1AR	4853	brca_tcga	2
1	VENHQS1BUi1BMUFSLTAxOmJyY2FfdGNnYQ	VENHQS1BUi1BMUFSOmJyY2FfdGNnYQ	brca_tcga_gistic	TCGA-AR-A1AR-01	TCGA-AR-A1AR	51205	brca_tcga	2
2	VENHQS1BUi1BMUFSLTAxOmJyY2FfdGNnYQ	VENHQS1BUi1BMUFSOmJyY2FfdGNnYQ	brca_tcga_gistic	TCGA-AR-A1AR-01	TCGA-AR-A1AR	100874392	brca_tcga	2
3	VENHQS1BUi1BMUFSLTAxOmJyY2FfdGNnYQ	VENHQS1BUi1BMUFSOmJyY2FfdGNnYQ	brca_tcga_gistic	TCGA-AR-A1AR-01	TCGA-AR-A1AR	284615	brca_tcga	2
4	VENHQS1BUi1BMUFSLTAxOmJyY2FfdGNnYQ	VENHQS1BUi1BMUFSOmJyY2FfdGNnYQ	brca_tcga_gistic	TCGA-AR-A1AR-01	TCGA-AR-A1AR	148741	brca_tcga	2
...	...	...	...	...	...	...	...	...
613540	VENHQS1FMi1BMUJDLTAxOmJyY2FfdGNnYQ	VENHQS1FMi1BMUJDOmJyY2FfdGNnYQ	brca_tcga_gistic	TCGA-E2-A1BC-01	TCGA-E2-A1BC	57606	brca_tcga	-2
613541	VENHQS1FMi1BMUJDLTAxOmJyY2FfdGNnYQ	VENHQS1FMi1BMUJDOmJyY2FfdGNnYQ	brca_tcga_gistic	TCGA-E2-A1BC-01	TCGA-E2-A1BC	201780	brca_tcga	-2
613542	VENHQS1FMi1BMUJDLTAxOmJyY2FfdGNnYQ	VENHQS1FMi1BMUJDOmJyY2FfdGNnYQ	brca_tcga_gistic	TCGA-E2-A1BC-01	TCGA-E2-A1BC	7006	brca_tcga	-2
613543	VENHQS1FMi1BMUJDLTAxOmJyY2FfdGNnYQ	VENHQS1FMi1BMUJDOmJyY2FfdGNnYQ	brca_tcga_gistic	TCGA-E2-A1BC-01	TCGA-E2-A1BC	326340	brca_tcga	-2
613544	VENHQS1FMi1BMUJDLTAxOmJyY2FfdGNnYQ	VENHQS1FMi1BMUJDOmJyY2FfdGNnYQ	brca_tcga_gistic	TCGA-E2-A1BC-01	TCGA-E2-A1BC	9750	brca_tcga	-2

613545 rows × 8 columns