R: CGDS-R : a library for accessing data in the MSKCC Cancer...

cgdsr-package {cgdsr} | R Documentation

## CGDS-R : a library for accessing data in the MSKCC Cancer Genomics Data Server (CGDS).

### Description

The package provides a basic set of R functions for querying the Cancer Genomics Data Server (CGDS), hosted by the Computational Biology Center at Memorial-Sloan-Kettering Cancer Center (MSKCC). Read more about this service at the cBio Cancer Genomics Portal, http://www.cbioportal.org/.

### Details

Package: | cgdsr
Type: | Package
License: | GPL
LazyLoad: | yes

The Cancer Genomic Data Server (CGDS) web service interface provides direct programmatic access to all genomic data stored within the server. This package provides a basic set of R functions for querying the CGDS hosted by the Computational Biology Center at Memorial-Sloan-Kettering Cancer Center (MSKCC).

The library can issue the following types of queries:

1. getCancerStudies(): What cancer studies are hosted on the server? For example TCGA Glioblastoma or TCGA Ovarian cancer.

2. getGeneticProfiles(): What genetic profile types are available for cancer study X? For example mRNA expression or copy number alterations.

3. getCaseLists(): what case sets are available for cancer study X? For example all samples or only samples corresponding to a given cancer subtype.

4. getProfileData(): Retrieve slices of genomic data. For example, a client can retrieve all mutation data from PTEN and EGFR in TCGA glioblastoma.

5. getClinicalData(): Retrieve clinical data (e.g. patient survival time and age) for a given case list.

### Author(s)

<jacobsen@cbio.mskcc.org>

### References

cBio Cancer Genomics Portal: http://www.cbioportal.org/

### See Also

`CGDS`, `getCancerStudies`, `getGeneticProfiles`, `getCaseLists`, `getProfileData`, `getClinicalData`.

### Examples

    # Create CGDS object
    mycgds = CGDS("http://www.cbioportal.org/")

    # Test the CGDS endpoint URL using a few simple API tests
    test(mycgds)

    # Get list of cancer studies at server
    getCancerStudies(mycgds)

    # Get available case lists (collection of samples) for a given cancer study
    mycancerstudy = getCancerStudies(mycgds)[2,1]
    mycaselist = getCaseLists(mycgds,mycancerstudy)[1,1]

    # Get available genetic profiles
    mygeneticprofile = getGeneticProfiles(mycgds,mycancerstudy)[4,1]

    # Get data slices for a specified list of genes, genetic profile and case list
    getProfileData(mycgds,c('BRCA1','BRCA2'),mygeneticprofile,mycaselist)

    # Get clinical data for the case list
    myclinicaldata = getClinicalData(mycgds,mycaselist)

[Package cgdsr version 1.2.10 Index]