getTCGAdata {UCSCXenaTools}

Get TCGA Common Data Sets by Project ID and Property

Description

This is the most useful function for user to download common TCGA datasets, it is similar to getFirehoseData function in RTCGAToolbox package.

Usage

getTCGAdata(
  project = NULL,
  clinical = TRUE,
  download = FALSE,
  forceDownload = FALSE,
  destdir = tempdir(),
  mRNASeq = FALSE,
  mRNAArray = FALSE,
  mRNASeqType = "normalized",
  miRNASeq = FALSE,
  exonRNASeq = FALSE,
  RPPAArray = FALSE,
  ReplicateBaseNormalization = FALSE,
  Methylation = FALSE,
  MethylationType = c("27K", "450K"),
  GeneMutation = FALSE,
  SomaticMutation = FALSE,
  GisticCopyNumber = FALSE,
  Gistic2Threshold = TRUE,
  CopyNumberSegment = FALSE,
  RemoveGermlineCNV = TRUE,
  ...
)

Arguments

project

default is NULL. Should be one or more of TCGA project id (character vector) provided by Xena. See all available project id, please use availTCGA("ProjectID").

clinical

logical. if TRUE, download clinical information. Default is TRUE.

download

logical. if TRUE, download data, otherwise return a result list include data information. Default is FALSE. You can set this to FALSE if you want to check what you will download or use other function provided by UCSCXenaTools to filter result datasets you want to download.

forceDownload

logical. if TRUE, force to download files no matter if exist. Default is FALSE.

destdir

specify a location to store download data. Default is system temp directory.

mRNASeq

logical. if TRUE, download mRNASeq data. Default is FALSE.

mRNAArray

logical. if TRUE, download mRNA microarray data. Default is FALSE.

mRNASeqType

character vector. Can be one, two or three in c("normalized", "pancan normalized", "percentile").

miRNASeq

logical. if TRUE, download miRNASeq data. Default is FALSE.

exonRNASeq

logical. if TRUE, download exon RNASeq data. Default is FALSE.

RPPAArray

logical. if TRUE, download RPPA data. Default is FALSE.

ReplicateBaseNormalization

logical. if TRUE, download RPPA data by Replicate Base Normalization (RBN). Default is FALSE.

Methylation

logical. if TRUE, download DNA Methylation data. Default is FALSE.

MethylationType

character vector. Can be one or two in c("27K", "450K").

GeneMutation

logical. if TRUE, download gene mutation data. Default is FALSE.

SomaticMutation

logical. if TRUE, download somatic mutation data. Default is FALSE.

GisticCopyNumber

logical. if TRUE, download Gistic2 Copy Number data. Default is FALSE.

Gistic2Threshold

logical. if TRUE, download Threshold Gistic2 data. Default is TRUE.

CopyNumberSegment

logical. if TRUE, download Copy Number Segment data. Default is FALSE.

RemoveGermlineCNV

logical. if TRUE, download Copy Number Segment data which has removed germline copy number variation. Default is TRUE.

...

other argument to download.file function

Details

TCGA Common Data Sets are frequently used for biological analysis. To make easier to achieve these data, this function provide really easy options to choose datasets and behavior. All availble information about datasets of TCGA can access vis availTCGA() and check with showTCGA().

Value

if download=TRUE, return data.frame from XenaDownload, otherwise return a list including XenaHub object and datasets information

Author(s)

Shixiang Wang [e-mail]

Examples

###### get data, but not download

# 1 choose project and data types you wanna download
getTCGAdata(project = "LUAD", mRNASeq = TRUE, mRNAArray = TRUE,
mRNASeqType = "normalized", miRNASeq = TRUE, exonRNASeq = TRUE,
RPPAArray = TRUE, Methylation = TRUE, MethylationType = "450K",
GeneMutation = TRUE, SomaticMutation = TRUE)

# 2 only choose 'LUAD' and its clinical data
getTCGAdata(project = "LUAD")
## Not run: 
###### download datasets

# 3 download clinical datasets of LUAD and LUSC
getTCGAdata(project = c("LUAD", "LUSC"), clinical = TRUE, download = TRUE)

# 4 download clinical, RPPA and gene mutation datasets of LUAD and LUSC
# getTCGAdata(project = c("LUAD", "LUSC"), clinical = TRUE, RPPAArray = TRUE, GeneMutation = TRUE)

## End(Not run)