This vignette is meant for those who wish to contribute to {cbioportalR}, or users who wish to gain an understanding of the inner-workings of {cbioportalR}.
We aim to keep returned data as close to raw API results as possible and avoid additional transformations/formatting. Because of this, data is not returned in tidy format. In the future we may consider removing non informative columns from results and returning everything as tibbles with clean names, but for now keeping data in raw format helps us be flexible to future cBioPortal API changes.
We try to limit internal API calls within functions that the user
did not explicitly ask for. In some places we deem it necessary to break
this (for example in .get_data_by_study() if a user passes
a study_id we look up the
molecular_profile_id), but we largely default to having
slightly less informative messages/checks in favor of fewer hidden
calls, as these can be problematic with slow internet or large data
sets.
cbp_api() internal function makes all api calls
(GET and POST using {httr} package). All other
user-facing or internal functions paste together necessary URLs and
query parameters based on the function and its arguments and pass to
this..get_data_by_study() and
.get_data_by_sample() are internal utility functions that
work for mutation/cna/fusion data pulls.*_by_study() query by study_id,
functions ending in *_by_sample() query by sample ID, and
functions ending in *_by_patient() query by patient
ID.available_*() and those starting with get_*().
These are named according to how you may use them in your workflow. For
example, you would check the available_profiles() for your
study_id in order to
get_fusions_by_study()