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


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Documentation for package ‘cgdsr’ version 1.3.0

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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.