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.
|Author||Mehmet Kemal Samur|
|Date of publication||None|
|Maintainer||Mehmet Kemal Samur <email@example.com>|
|License||GPL (>= 2)|
CorResult-class: An S4 class to store correlations between gene expression...
DGEResult-class: An S4 class to store differential gene expression results
FirehoseCGHArray-class: An S4 class to store data from CGA platforms
FirehoseData-class: An S4 class to store main data object from clinent function.
FirehoseGISTIC-class: An S4 class to store processed copy number data. (Data...
FirehoseMethylationArray-class: An S4 class to store data from methylation platforms
FirehosemRNAArray-class: An S4 class to store data from array (mRNA, miRNA etc.)...
getCNGECorrelation: Perform correlation analysis betwwen gene expression and copy...
getData: Export data from FirehoseData object
getData-methods: Export data from FirehoseData object
getDiffExpressedGenes: Perform differential gene expression analysis for mRNA...
getFirehoseAnalyzeDates: Get data analyze dates.
getFirehoseData: Get data from Firehose portal.
getFirehoseDatasets: Get list of TCGA cohorts.
getFirehoseRunningDates: Get standard data running dates.
getMutationRate: Make a table for mutation rate of each gene in the cohort
getReport: Draws a circle plot into working directory
getSurvival: Perform survival analysis based on gene expression data
hg19.ucsc.gene.locations: Gene coordinates for circle plot.
RTCGASample: A sample data object for sample codes.
RTCGAToolbox: RTCGAToolbox: A New Tool for Exporting TCGA Firehose Data
showResults: Export toptable or correlation data frame
showResults-CorResult: Export toptable or correlation data frame
showResults-DGEResult: Export toptable or correlation data frame