cgdsr (version 1.3.0)

cgdsr-package: 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.

References

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

See Also

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

Examples

# NOT RUN {
# 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)
# }