getDataTCGA: getDataTCGA

View source: R/getDataTCGA.R

getDataTCGAR Documentation

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.