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


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Documentation for package ‘cgdsr’ version 1.1

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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.