getDataTCGA: getDataTCGA

In ibsquare/MoonlightR: Identify oncogenes and tumor suppressor genes from omics data

getDataTCGA

Description

This function retrieves and prepares TCGA data

Usage

getDataTCGA(
  cancerType,
  dataType,
  directory,
  cor.cut = 0.6,
  qnt.cut = 0.25,
  nSample,
  stage = "ALL",
  subtype = 0,
  samples = NULL
)

Arguments

cancerType	select cancer type for which analysis should be run. panCancer for all available cancer types in TCGA. Defaults to panCancer
dataType	is dataType such as gene expression, cnv, methylation etc.
directory	Directory/Folder where the data was downloaded. Default: GDCdata
cor.cut	cor.cut
qnt.cut	qnt.cut
nSample	nSample
stage	stage
subtype	subtype
samples	samples

Value

returns filtered TCGA data

Examples

## Not run: 
dataFilt <- getDataTCGA(cancerType = "LUAD",
dataType = "Gene expression", directory = "data", nSample = 4)

## End(Not run)

ibsquare/MoonlightR documentation built on May 19, 2024, 6:16 a.m.