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

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).

Author
Anders Jacobsen <jacobsen@cbio.mskcc.org>
Date of publication
2015-08-27 08:38:53
Maintainer
Augustin Luna <lunaa@cbio.mskcc.org>
License
LGPL-3
Version
1.2.5
URLs

View on CRAN

Man pages

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...
cgdsr-getMutationData
Get mutation data for cancer study
cgdsr-getProfileData
Retrieves genomic profile data for genes and genetic...
cgdsr-package
CGDS-R : a library for accessing data in the MSKCC Cancer...
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.

Files in this package

cgdsr
cgdsr/inst
cgdsr/inst/tests
cgdsr/inst/tests/test_cgdsr.R
cgdsr/inst/doc
cgdsr/inst/doc/cgdsr.Rnw
cgdsr/inst/doc/cgdsr.R
cgdsr/inst/doc/cgdsr.pdf
cgdsr/tests
cgdsr/tests/runTests.R
cgdsr/NAMESPACE
cgdsr/R
cgdsr/R/cgdsr.R
cgdsr/vignettes
cgdsr/vignettes/cgdsr.Rnw
cgdsr/MD5
cgdsr/build
cgdsr/build/vignette.rds
cgdsr/DESCRIPTION
cgdsr/man
cgdsr/man/cgdsr-setVerbose.Rd
cgdsr/man/cgdsr-getCancerStudies.Rd
cgdsr/man/cgdsr-test.Rd
cgdsr/man/cgdsr-getClinicalData.Rd
cgdsr/man/cgdsr-package.Rd
cgdsr/man/cgdsr-getProfileData.Rd
cgdsr/man/cgdsr-processURL.Rd
cgdsr/man/cgdsr-getCaseLists.Rd
cgdsr/man/cgdsr-getMutationData.Rd
cgdsr/man/cgdsr-setPlotErrorMsg.Rd
cgdsr/man/cgdsr-CGDS.Rd
cgdsr/man/cgdsr-plot.Rd
cgdsr/man/cgdsr-getGeneticProfiles.Rd