FirehoseGISTIC-class: An S4 class to store processed copy number data. (Data...

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

An S4 class to store processed copy number data. (Data processed by using GISTIC2 algorithm)

Description

An S4 class to store processed copy number data. (Data processed by using GISTIC2 algorithm)

Usage

## S4 method for signature 'FirehoseGISTIC'
isEmpty(x)

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

Arguments

x	A FirehoseGISTIC class object
object	A FirehoseGISTIC object
...	additional arguments for updateObject
verbose	logical (default FALSE) whether to print extra messages

Methods (by generic)

• isEmpty(FirehoseGISTIC): check whether the FirehoseGISTIC object has data in it or not

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

Slots

Dataset

Cohort name

AllByGene

A data frame that stores continuous copy number

ThresholdedByGene

A data frame for discrete copy number data

Peaks

A data frame storing GISTIC peak data. See getGISTICPeaks.

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