Quick Reference

To see help pages while you work type:

help(function)

example:

help(fetch_rows)

Import available cdapython functions¶

In [2]:

from cdapython import tables, columns, column_values, fetch_rows, summary_counts

from cdapython import tables, columns, column_values, fetch_rows, summary_counts

Get a list of searchable CDA tables¶

In [3]:

tables()

tables()

Out[3]:

['diagnosis',
 'file',
 'mutation',
 'researchsubject',
 'specimen',
 'subject',
 'treatment']

Explore CDA tables' columns in detail¶

In [4]:

columns()

columns()

Out[4]:

Loading ITables v2.4.0 from the init_notebook_mode cell... (need help?)

See what values are populated in a given column¶

In [5]:

column_values( 'primary_diagnosis_site' )

column_values( 'primary_diagnosis_site' )

Out[5]:

Loading ITables v2.4.0 from the init_notebook_mode cell... (need help?)

Fetch subject row summary information for a column value¶

In [6]:

summary_counts( table= 'subject', match_all = 'primary_diagnosis_site = kid*')

summary_counts( table= 'subject', match_all = 'primary_diagnosis_site = kid*')

╔═════════════════════════╗
║ total_subject_matches   ║
╠═════════════════════════╣
║ 2738                    ║
╚═════════════════════════╝
╔═══════════════════════╗
║ total_related_files   ║
╠═══════════════════════╣
║ 556489                ║
╚═══════════════════════╝
╔═════════╦═══════════════════════╗
║   count ║ subject_data_source   ║
╠═════════╬═══════════════════════╣
║    2436 ║ GDC                   ║
║    1388 ║ IDC                   ║
║     269 ║ PDC                   ║
║     213 ║ CDS                   ║
║       1 ║ ICDC                  ║
╚═════════╩═══════════════════════╝
╔═════════╦════════╗
║   count ║ sex    ║
╠═════════╬════════╣
║    1659 ║ male   ║
║    1077 ║ female ║
║       2 ║ <NA>   ║
╚═════════╩════════╝
╔═════════╦═══════════════════════════════════════════╗
║   count ║ race                                      ║
╠═════════╬═══════════════════════════════════════════╣
║    1607 ║ White                                     ║
║     808 ║ <NA>                                      ║
║     277 ║ Black or African American                 ║
║      43 ║ Asian                                     ║
║       2 ║ American Indian or Alaska Native          ║
║       1 ║ Native Hawaiian or Other Pacific Islander ║
╚═════════╩═══════════════════════════════════════════╝
╔═════════╦════════════════════╗
║   count ║ ethnicity          ║
╠═════════╬════════════════════╣
║    1353 ║ Non-Hispanic       ║
║    1254 ║ <NA>               ║
║     131 ║ Hispanic or Latino ║
╚═════════╩════════════════════╝
╔═════════╦══════════════════════════╗
║   count ║ cause_of_death           ║
╠═════════╬══════════════════════════╣
║    2563 ║ <NA>                     ║
║     155 ║ Cancer-Related Death     ║
║       7 ║ Infection                ║
║       7 ║ Toxicity                 ║
║       4 ║ Non-Cancer Related Death ║
║       1 ║ Cardiovascular Disorder  ║
║       1 ║ Surgical Complication    ║
╚═════════╩══════════════════════════╝

Fetch rows from any table for a column value¶

subject dataresearch subject dataspecimen datadiagnosis datatreatment datamutation data

fetch_rows( table= "subject", match_all='primary_diagnosis_site = kid*' )

fetch_rows( table= "researchsubject", match_all='primary_diagnosis_site = kid*' )

fetch_rows( table= "specimen", match_all='primary_diagnosis_site = kid*' )

fetch_rows( table= "diagnosis", match_all='primary_diagnosis_site = kid*' )

fetch_rows( table= "treatment", match_all='primary_diagnosis_site = kid*' )

fetch_rows( table= "mutation", match_all='primary_diagnosis_site = kid*' )

Fetch subject rows for a column value¶

In [7]:

fetch_rows( table= 'mutation', match_all = 'subject_id = TCGA.TCGA-04-1369')

fetch_rows( table= 'mutation', match_all = 'subject_id = TCGA.TCGA-04-1369')

Out[7]:

Loading ITables v2.4.0 from the init_notebook_mode cell... (need help?)