get_samples_by_patient

Get sample IDs for a given set of patient IDs

Provides R users with direct access to genomic and clinical data from the 'cBioPortal' web resource via user-friendly
functions that wrap 'cBioPortal's' existing API endpoints <https://www.cbioportal.org/api/swagger-ui/index.html>. Users can browse and query genomic data on mutations,
copy number alterations and fusions, as well as data on tumor mutational burden ('TMB'),
microsatellite instability status ('MSI'), 'FACETS' and select clinical data points (depending on the study).
See <https://www.cbioportal.org/> and Gao et al., (2013) <doi:10.1126/scisignal.2004088> for more information on the cBioPortal web resource.

Karissa Whiting

cbioportalR

Browse and Query Clinical and Genomic Data from cBioPortal

get_samples_by_patient function

<dl><dt>patient_id</dt>
<dd>A character string of sample IDs to query</dd>
<dt>study_id</dt>
<dd>A character string indicating which study ID should be searched.
Only 1 study allowed. If NULL, we will guess a default study ID based on your database URL.</dd>
<dt>base_url</dt>
<dd>The database URL to query
If <code>NULL</code> will default to URL set with <code>set_cbioportal_db(&lt;your_db&gt;)</code></dd></dl>

Arguments

Get sample IDs for a given set of patient IDs — get_samples_by_patient

<dl>

<dt>patient_id</dt>
<dd>A character string of sample IDs to query</dd>


<dt>study_id</dt>
<dd>A character string indicating which study ID should be searched.
Only 1 study allowed. If NULL, we will guess a default study ID based on your database URL.</dd>


<dt>base_url</dt>
<dd>The database URL to query
If <code>NULL</code> will default to URL set with <code>set_cbioportal_db(&lt;your_db&gt;)</code></dd>

</dl>

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get_samples_by_patient: Get sample IDs for a given set of patient IDs

Description

Usage

Value

Arguments

Examples