FirehoseGISTIC-class


An S4 class to store processed copy number data. (Data processed by using GISTIC2 algorithm)


Managing data from large scale projects such as The Cancer Genome
Atlas (TCGA) for further analysis is an important and time consuming step
for research projects. Several efforts, such as Firehose project, make TCGA
pre-processed data publicly available via web services and data portals but
it requires managing, downloading and preparing the data for following
steps. We developed an open source and extensible R based data client for
Firehose pre-processed data and demonstrated its use with sample case
studies. Results showed that RTCGAToolbox could improve data management for
researchers who are interested with TCGA data. In addition, it can be
integrated with other analysis pipelines for following data analysis.

Mehmet Kemal Samur

RTCGAToolbox

A new tool for exporting TCGA Firehose data

FirehoseGISTIC-class function

 <dl>
<dt><code>Dataset</code></dt><dd>Cohort name</dd> <dt><code>AllByGene</code></dt><dd>A data frame that stores continuous copy number</dd> <dt><code>ThresholedByGene</code></dt><dd>A data frame for discrete copy number data</dd> </dl>

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An S4 class to store processed copy number data. (Data processed by using GISTIC2 algorithm)

FirehoseGISTIC-class: An S4 class to store processed copy number data. (Data processed by using GISTIC2 algorithm)

Description

Arguments

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