FirehoseData-class: Class '"FirehoseData"'

In RTCGAToolbox: A new tool for exporting TCGA Firehose data

Description

This class is the main output of Firehose data client. All data will be downloaded as a FirehoseData class.

Objects from the Class

Objects can be created by calls of the form new("FirehoseData", ...).

Slots

Dataset:

Object of class "character": Name of the TCGA dataset.

Clinical:

Object of class "data.frame": Clinical dataset.

RNASeqGene:

Object of class "matrix": Gene level RNASeq data. Data could be either raw counts or normalized.

RNASeq2GeneNorm:

Object of class "matrix": Gene level RNASeq2 data. Firehose has 2 pre process pipeline for RNASeq data. More information can be accessible from Firehoseproject web site. Data could be either raw counts or normalized.

miRNASeqGene:

Object of class "matrix": miRNA expression data from RNA seq platrom. Data could be either normalized or raw counts.

CNASNP:

Object of class "data.frame": Segmented copy number altereration data from SNP array.

CNVSNP:

Object of class "data.frame": Segmented copy number variations data from SNP array.

CNAseq:

Object of class "data.frame": Segmented copy number alteration data from sequencing data.

CNACGH:

Object of class "list": Lsit of segmented copy number alterations data from CGH array.

Methylation:

Object of class "list": List of methylation array data. Each member of the list will be data from different platform.

mRNAArray:

Object of class "list": List of mRNA expression data object. Each member of the list will be data from different platform.

miRNAArray:

Object of class "list": List of miRNA expression data object. Each member of the list will be data from different platform.

RPPAArray:

Object of class "list": List of RPPAArray data object. Each member of the list will be data from different platform.

Mutations:

Object of class "data.frame": Mutation data related with samples.

GISTIC:

Object of class "FirehoseGISTIC": Processed copy number estimations from GISTIC output of Firehose project.

Methods

No methods defined with class "FirehoseData" in the signature.

Author(s)

Mehmet Kemal Samur

Examples

showClass("FirehoseData")

RTCGAToolbox documentation built on May 2, 2019, 5:16 p.m.