cgdsr: R-Based API for Accessing the MSKCC Cancer Genomics Data Server (CGDS)
Version 1.2.6

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).

Browse man pages Browse package API and functions Browse package files

AuthorAnders Jacobsen <jacobsen@cbio.mskcc.org>
Date of publication2017-04-11 12:22:10 UTC
MaintainerAugustin Luna <lunaa@cbio.mskcc.org>
LicenseLGPL-3
Version1.2.6
URL https://github.com/cBioPortal/cgdsr
Package repositoryView on CRAN
InstallationInstall the latest version of this package by entering the following in R:
install.packages("cgdsr")

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.

Functions

CGDS Man page
cgdsr Man page
cgdsr-CGDS Man page
cgdsr-getCancerStudies Man page
cgdsr-getCaseLists Man page
cgdsr-getClinicalData Man page
cgdsr-getGeneticProfiles Man page
cgdsr-getMutationData Man page
cgdsr-getProfileData Man page
cgdsr-package Man page
cgdsr-plot Man page
cgdsr-processURL Man page
cgdsr-setPlotErrorMsg Man page
cgdsr-setVerbose Man page
cgdsr-test Man page
getCancerStudies Man page
getCancerStudies.CGDS Man page
getCaseLists Man page
getCaseLists.CGDS Man page
getClinicalData Man page
getClinicalData.CGDS Man page
getGeneticProfiles Man page
getGeneticProfiles.CGDS Man page
getMutationData Man page
getMutationData.CGDS Man page
getProfileData Man page
getProfileData.CGDS Man page
plot Man page
plot.CGDS Man page
processURL Man page
processURL.CGDS Man page
setPlotErrorMsg Man page
setPlotErrorMsg.CGDS Man page
setVerbose Man page
setVerbose.CGDS Man page
test Man page
test.CGDS Man page

Files

inst
inst/tests
inst/tests/test_cgdsr.R
inst/doc
inst/doc/cgdsr.Rnw
inst/doc/cgdsr.R
inst/doc/cgdsr.pdf
tests
tests/runTests.R
NAMESPACE
R
R/cgdsr.R
vignettes
vignettes/cgdsr.Rnw
MD5
build
build/vignette.rds
DESCRIPTION
man
man/cgdsr-setVerbose.Rd
man/cgdsr-getCancerStudies.Rd
man/cgdsr-test.Rd
man/cgdsr-getClinicalData.Rd
man/cgdsr-package.Rd
man/cgdsr-getProfileData.Rd
man/cgdsr-processURL.Rd
man/cgdsr-getCaseLists.Rd
man/cgdsr-getMutationData.Rd
man/cgdsr-setPlotErrorMsg.Rd
man/cgdsr-CGDS.Rd
man/cgdsr-plot.Rd
man/cgdsr-getGeneticProfiles.Rd
cgdsr documentation built on May 19, 2017, 8:58 p.m.