FirehoseData-class


An S4 class to store main data object from clinent function.


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

FirehoseData-class function

 <dl>
<dt><code>Dataset</code></dt><dd>A cohort name</dd> <dt><code>Clinical</code></dt><dd>Clinical data frame</dd> <dt><code>RNASeqGene</code></dt><dd>Gene level expression data matrix from RNAseq</dd> <dt><code>RNASeq2GeneNorm</code></dt><dd>Gene level expression data matrix from RNAseq (RSEM)</dd> <dt><code>miRNASeqGene</code></dt><dd>miRNA expression data from matrix smallRNAseq</dd> <dt><code>CNASNP</code></dt><dd>A data frame to store somatic copy number alterations from SNP array platform</dd> <dt><code>CNVSNP</code></dt><dd>A data frame to store germline copy number variants from SNP array platform</dd> <dt><code>CNAseq</code></dt><dd>A data frame to store somatic copy number alterations from sequencing platform</dd> <dt><code>CNACGH</code></dt><dd>A list that stores <code>FirehoseCGHArray</code> object for somatic copy number alterations from CGH platform</dd> <dt><code>Methylation</code></dt><dd>A list that stores <code>FirehoseMethylationArray</code> object for methylation data</dd> <dt><code>mRNAArray</code></dt><dd>A list that stores <code>FirehosemRNAArray</code> object for gene expression data from microarray</dd> <dt><code>miRNAArray</code></dt><dd>A list that stores <code>FirehosemRNAArray</code> object for miRNA expression data from microarray</dd> <dt><code>RPPAArray</code></dt><dd>A list that stores <code>FirehosemRNAArray</code> object for RPPA data</dd> <dt><code>Mutations</code></dt><dd>A data frame for mutation infromation from sequencing data</dd> <dt><code>GISTIC</code></dt><dd>A <code>FirehoseGISTIC</code> object to store processed copy number data</dd> <dt><code>BarcodeUUID</code></dt><dd>A data frame that stores the Barcodes, UUIDs and Short sample identifiers</dd> </dl>

Slots

An S4 class to store main data object from clinent function.

FirehoseData-class: An S4 class to store main data object from clinent function.

Description

Arguments

Slots