# R-Based API for Accessing the MSKCC Cancer Genomics Data Server (CGDS)

## Documentation for package ‘cgdsr’ version 1.3.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

cgdsr-package | CGDS-R : a library for accessing data in the MSKCC Cancer Genomics Data Server (CGDS).
CGDS | Construct a CGDS connection object
cgdsr | CGDS-R : a library for accessing data in the MSKCC Cancer Genomics Data Server (CGDS).
cgdsr-CGDS | Construct a CGDS connection object
cgdsr-getCancerStudies | Get available cancer studies available in CGDS
cgdsr-getCaseLists | Get available case lists for a specific cancer study
cgdsr-getClinicalData | Get clinical data for cancer study
cgdsr-getGeneticProfiles | Get available genetic data profiles for a specific cancer study
cgdsr-getMutationData | Get mutation data for cancer study
cgdsr-getProfileData | Retrieves genomic profile data for genes and genetic profiles.
cgdsr-plot | Generic plot function for CGDS API data.
cgdsr-processURL | Internal methods for CGDS library.
cgdsr-setPlotErrorMsg | Set custom plot error message
cgdsr-setVerbose | Set verbose logging level for CGDS function calls
cgdsr-test | Simple test suite for CGDS object.
getCancerStudies | Get available cancer studies available in CGDS
getCancerStudies.CGDS | Get available cancer studies available in CGDS
getCaseLists | Get available case lists for a specific cancer study
getCaseLists.CGDS | Get available case lists for a specific cancer study
getClinicalData | Get clinical data for cancer study
getClinicalData.CGDS | Get clinical data for cancer study
getGeneticProfiles | Get available genetic data profiles for a specific cancer study
getGeneticProfiles.CGDS | Get available genetic data profiles for a specific cancer study
getMutationData | Get mutation data for cancer study
getMutationData.CGDS | Get mutation data for cancer study
getProfileData | Retrieves genomic profile data for genes and genetic profiles.
getProfileData.CGDS | Retrieves genomic profile data for genes and genetic profiles.
plot | Generic plot function for CGDS API data.
plot.CGDS | Generic plot function for CGDS API data.
processURL | Internal methods for CGDS library.
processURL.CGDS | Internal methods for CGDS library.
setPlotErrorMsg | Set custom plot error message
setPlotErrorMsg.CGDS | Set custom plot error message
setVerbose | Set verbose logging level for CGDS function calls
setVerbose.CGDS | Set verbose logging level for CGDS function calls
test | Simple test suite for CGDS object.
test.CGDS | Simple test suite for CGDS object.