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

In mksamur/RTCGAToolbox: A new tool for exporting TCGA Firehose data

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

Description

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

Usage

## S4 method for signature 'FirehoseData'
show(object)

## S4 method for signature 'FirehoseData'
getData(object, type, platform)

## S4 method for signature 'FirehoseGISTIC'
getData(object, type, platform)

## S4 method for signature 'ANY'
getData(object, type, platform)

## S4 method for signature 'FirehoseData'
updateObject(object, ..., verbose = FALSE)

## S4 method for signature 'FirehoseData'
selectType(object, dataType)

Arguments

object	A FirehoseData object
type	A data type to be extracted
platform	An index for data types that may come from multiple platforms (such as mRNAArray), for GISTIC data, one of the options: 'AllByGene', 'ThresholdedByGene', or 'Peaks'
...	additional arguments for updateObject
verbose	logical (default FALSE) whether to print extra messages
dataType	An available data type, see object show method

Methods (by generic)

• show(FirehoseData): show method

• getData(FirehoseData): Get a matrix or data.frame from FirehoseData

• getData(FirehoseGISTIC): Get GISTIC data from FirehoseData

• getData(ANY): Default method for getting data from FirehoseData

• updateObject(FirehoseData): Update an old RTCGAToolbox FirehoseData object to the most recent API

• selectType(FirehoseData): Extract data type

Slots

Dataset

A cohort name

runDate

Standard data run date from getFirehoseRunningDates

gistic2Date

Analyze running date from getFirehoseAnalyzeDates

clinical

clinical data frame

RNASeqGene

Gene level expression data matrix from RNAseq

RNASeq2Gene

Gene level expression data matrix from RNAseqV2

RNASeq2GeneNorm

Gene level expression data matrix from RNAseqV2 (RSEM)

miRNASeqGene

miRNA expression data from matrix smallRNAseq

CNASNP

A data frame to store somatic copy number alterations from SNP array platform

CNVSNP

A data frame to store germline copy number variants from SNP array platform

CNASeq

A data frame to store somatic copy number alterations from sequencing platform

CNACGH

A list that stores FirehoseCGHArray object for somatic copy number alterations from CGH platform

Methylation

A list that stores FirehoseMethylationArray object for methylation data

mRNAArray

A list that stores FirehosemRNAArray object for gene expression data from microarray

miRNAArray

A list that stores FirehosemRNAArray object for miRNA expression data from microarray

RPPAArray

A list that stores FirehosemRNAArray object for RPPA data

Mutation

A data frame for mutation infromation from sequencing data

GISTIC

A FirehoseGISTIC object to store processed copy number data

BarcodeUUID

A data frame that stores the Barcodes, UUIDs and Short sample identifiers

mksamur/RTCGAToolbox documentation built on Oct. 29, 2023, 10:06 p.m.