VCF and image files available for the same patients¶

I'm a cancer researcher, and I have a hypothesis that I can correlate a specific mutation with a specific kidney cancer morphology. I'm looking for subjects that have kidney cancer with both CT and sequencing data that I might be able to incorporate into my research.

First, decide what column to search. I'm looking for columns that have to do with file type:

In [2]:

columns(table="file")

columns(table="file")

Out[2]:

Loading ITables v2.8.1 from the init_notebook_mode cell... (need help?)

In [3]:

column_values("file_type")

column_values("file_type")

Out[3]:

Loading ITables v2.8.1 from the init_notebook_mode cell... (need help?)

CT image storage and annotated somatic mutation files should give me the data I want. Now to find a column to seperate out the kidney cancer subjects:

In [4]:

columns()

columns()

Out[4]:

Loading ITables v2.8.1 from the init_notebook_mode cell... (need help?)

In [5]:

column_values("anatomic_site", filters= "*kidney*" )

column_values("anatomic_site", filters= "*kidney*" )

Out[5]:

Loading ITables v2.8.1 from the init_notebook_mode cell... (need help?)

Looks like there are lots of kidney patients, however kidney has been specified a few different ways, so I'll have to search with a wildcard. This makes my three search parameters:

• 'anatomic_site = *kidney' (the * means match anything that ends with kidney no matter what words or letters are after it.)

• 'file_type = CT Image Storage'

• 'file_type = Annotated Somatic Mutation'

But if I run a search with file_type in it twice, it will only give me back files that are both a CT Image Storage AND an Annotated Somatic Mutation. No one file can be both of those things, so what I will really want is to do two searches, one for kidney and CT:

get_subject_data(match_all=['anatomic_site = *kidney', 'file_type = CT Image Storage'])

and one for kidney and mutation:

get_subject_data(match_all=['anatomic_site = *kidney', 'file_type = Annotated Somatic Mutation'])

and then combine the results.

I want subject data, so I'll search by subject, and I'll add the file data on so I know where to get the files. Again * means "anything" so doing add_columns = "file.*" will add all the file columns.

So all together we have

Get the results for each search and save them in variables:

In [6]:

CT = get_subject_data(match_all=['anatomic_site = *kidney', 'file_type = CT Image Storage'], add_columns="file.*")
mutation = get_subject_data(match_all=['anatomic_site = *kidney', 'file_type = Annotated Somatic Mutation'], add_columns="file.*")

CT = get_subject_data(match_all=['anatomic_site = *kidney', 'file_type = CT Image Storage'], add_columns="file.*") mutation = get_subject_data(match_all=['anatomic_site = *kidney', 'file_type = Annotated Somatic Mutation'], add_columns="file.*")

get the intersection of the results:

In [7]:

CTmutation = intersect_subject_results(CT, mutation)
CTmutation

CTmutation = intersect_subject_results(CT, mutation) CTmutation

Out[7]:

Loading ITables v2.8.1 from the init_notebook_mode cell... (need help?)