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cgdsr (version 1.1.30)

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

Description

The package 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).

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Version

Install

install.packages('cgdsr')

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Version

1.1.30

License

GPL

Maintainer

Anders Jacobsen

Last Published

September 17th, 2013

Functions in cgdsr (1.1.30)

cgdsr-setVerbose

Set verbose logging level for CGDS function calls

cgdsr-getClinicalData

Get clinical data for cancer study

cgdsr-CGDS

Construct a CGDS connection object

cgdsr-test

Simple test suite for CGDS object.

cgdsr-getCaseLists

Get available case lists for a specific cancer study

cgdsr-getMutationData

Get mutation data for cancer study

cgdsr-plot

Generic plot function for CGDS API data.

cgdsr-getProfileData

Retrieves genomic profile data for genes and genetic profiles.

cgdsr-processURL

Internal methods for CGDS library.

cgdsr-getGeneticProfiles

Get available genetic data profiles for a specific cancer study

cgdsr-getCancerStudies

Get available cancer studies available in CGDS

cgdsr-package

CGDS-R : a library for accessing data in the MSKCC Cancer Genomics Data Server (CGDS).

cgdsr-setPlotErrorMsg

Set custom plot error message