Get TCGA Common Data Sets by Project ID and Property

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

Value

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

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().

Author

Shixiang Wang w_shixiang@163.com

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)
#> $Xena
#> class: XenaHub 
#> hosts():
#>   https://tcga.xenahubs.net
#> cohorts() (1 total):
#>   TCGA Lung Adenocarcinoma (LUAD)
#> datasets() (7 total):
#>   TCGA.LUAD.sampleMap/HumanMethylation450
#>   TCGA.LUAD.sampleMap/HiSeqV2
#>   TCGA.LUAD.sampleMap/miRNA_HiSeq_gene
#>   ...
#>   TCGA.LUAD.sampleMap/AgilentG4502A_07_3
#>   TCGA.LUAD.sampleMap/HiSeqV2_exon
#> 
#> $DataInfo
#> # A tibble: 7 × 20
#>   XenaHosts XenaHostNames XenaCohorts XenaDatasets SampleCount DataSubtype Label
#>   <chr>     <chr>         <chr>       <chr>              <int> <chr>       <chr>
#> 1 https://… tcgaHub       TCGA Lung … TCGA.LUAD.s…         492 DNA methyl… Meth…
#> 2 https://… tcgaHub       TCGA Lung … TCGA.LUAD.s…         576 gene expre… Illu…
#> 3 https://… tcgaHub       TCGA Lung … TCGA.LUAD.s…         495 miRNA matu… Illu…
#> 4 https://… tcgaHub       TCGA Lung … TCGA.LUAD.s…         706 phenotype   Phen…
#> 5 https://… tcgaHub       TCGA Lung … TCGA.LUAD.s…          NA protein ex… RPPA 
#> 6 https://… tcgaHub       TCGA Lung … TCGA.LUAD.s…          33 gene expre… Agil…
#> 7 https://… tcgaHub       TCGA Lung … TCGA.LUAD.s…         576 exon expre… Illu…
#> # ℹ 13 more variables: Type <chr>, AnatomicalOrigin <chr>, SampleType <chr>,
#> #   Tags <chr>, ProbeMap <chr>, LongTitle <chr>, Citation <chr>, Version <chr>,
#> #   Unit <chr>, Platform <chr>, ProjectID <chr>, DataType <chr>, FileType <chr>
#> 

# 2 only choose 'LUAD' and its clinical data
getTCGAdata(project = "LUAD")
#> $Xena
#> class: XenaHub 
#> hosts():
#>   https://tcga.xenahubs.net
#> cohorts() (1 total):
#>   TCGA Lung Adenocarcinoma (LUAD)
#> datasets() (1 total):
#>   TCGA.LUAD.sampleMap/LUAD_clinicalMatrix
#> 
#> $DataInfo
#> # A tibble: 1 × 20
#>   XenaHosts XenaHostNames XenaCohorts XenaDatasets SampleCount DataSubtype Label
#>   <chr>     <chr>         <chr>       <chr>              <int> <chr>       <chr>
#> 1 https://… tcgaHub       TCGA Lung … TCGA.LUAD.s…         706 phenotype   Phen…
#> # ℹ 13 more variables: Type <chr>, AnatomicalOrigin <chr>, SampleType <chr>,
#> #   Tags <chr>, ProbeMap <chr>, LongTitle <chr>, Citation <chr>, Version <chr>,
#> #   Unit <chr>, Platform <chr>, ProjectID <chr>, DataType <chr>, FileType <chr>
#> 
if (FALSE) {
###### 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)
}