R-Based API for accessing the MSKCC Cancer Genomics Data Server (CGDS).

Documentation for package ‘cgdsr’ version 1.1

DESCRIPTION file.
Overview of user guides and package vignettes; browse directory.

Help Pages

cgdsr-package	CGDS-R : a library for accessing the MSKCC Cancer Genomics Data Server (CGDS).
CGDS	Construct a CGDS connection object
cgdsr	CGDS-R : a library for accessing the MSKCC Cancer Genomics Data Server (CGDS).
cgdsr-CGDS	Construct a CGDS connection object
cgdsr-getCancerTypes	Get available cancer types available in CGDS
cgdsr-getCaseLists	Get available case lists for a specific cancer type
cgdsr-getGeneticProfiles	Get available genetic data profiles for a specific cancer type
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-setVerbose	Set verbose logging level for CGDS function calls
cgdsr-test	Simple test suite for CGDS object.
getCancerTypes	Get available cancer types available in CGDS
getCancerTypes.CGDS	Get available cancer types available in CGDS
getCaseLists	Get available case lists for a specific cancer type
getCaseLists.CGDS	Get available case lists for a specific cancer type
getGeneticProfiles	Get available genetic data profiles for a specific cancer type
getGeneticProfiles.CGDS	Get available genetic data profiles for a specific cancer type
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.
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.