Man pages for mksamur/RTCGAToolbox
A new tool for exporting TCGA Firehose data
| accmini | A subset of the Adrenocortical Carcinoma (ACC) dataset |
| biocExtract | Extract and convert data from a 'FirehoseData' object to a... |
| 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.)... |
| getBroadSubtypes | Download expression-based cancer subtypes from the Broad... |
| getData | Extract data from FirehoseData object |
| getFirehoseAnalyzeDates | Get data analyze dates. |
| getFirehoseData | Get data from Firehose portal. |
| getFirehoseDatasets | Get a list of TCGA disease cohorts |
| getFirehoseRunningDates | Get standard data running dates. |
| getGISTICPeaks | Download GISTIC2 peak-level data from the Firehose pipeline |
| getLinks | Get resource links from inputs |
| getMutationRate | Make a table for mutation rate of each gene in the cohort |
| hg19.ucsc.gene.locations | Gene coordinates for circle plot. |
| makeSummarizedExperimentFromGISTIC | Create a SummarizedExperiment from FireHose GISTIC |
| RTCGAToolbox | RTCGAToolbox: A New Tool for Exporting TCGA Firehose Data |
| selectType | Accessor function for the FirehoseData object |
| showResults | Export toptable or correlation data frame |
| showResults-CorResult | Export toptable or correlation data frame |
| showResults-DGEResult | Export toptable or correlation data frame |
