TCGAbiolinks (version 1.2.5)

TCGAquery: Searches TCGA open-access data providing also latest version of the files.

Description

The TCGAquery searches TCGA open-access data through a preprocessed table with the latest version of the files.

Some parameters as tumor, platorm, level, center, barcode can be used to search the data.

TCGAquery will return a matrix with the results found, that will be used in the other function TCGAdownload, TCGAprepare.

Usage

TCGAquery(tumor = NULL, platform = NULL, samples = NULL, center = NULL, level = NULL, version = NULL)

Arguments

tumor

Disease Examples:

OV	BRCA	CESC	ESCA
PCPG	LUSC	LGG	SKCM
KICH	CHOL	GBM	UCEC
PRAD	PAAD	THYM	KIRC
THCA	SARC	LAML	TGCT
COAD	KIRP	HNSC	ACC
UVM	READ	BLCA	DLBC
UCS	FPPP	OV	BRCA

platform

Example:

CGH- 1x1M_G4447A

IlluminaGA_RNASeqV2

AgilentG4502A_07

IlluminaGA_mRNA_DGE

Human1MDuo

HumanMethylation450

HG-CGH-415K_G4124A

IlluminaGA_miRNASeq

HumanHap550

IlluminaHiSeq_miRNASeq

ABI

H-miRNA_8x15K

HG-CGH-244A

SOLiD_DNASeq

IlluminaDNAMethylation_OMA003_CPI

IlluminaGA_DNASeq_automated

IlluminaDNAMethylation_OMA002_CPI

HG-U133_Plus_2

HuEx- 1_0-st-v2

Mixed_DNASeq

H-miRNA_8x15Kv2

IlluminaGA_DNASeq_curated

MDA_RPPA_Core

IlluminaHiSeq_TotalRNASeqV2

HT_HG-U133A

IlluminaHiSeq_DNASeq_automated

diagnostic_images

microsat_i

IlluminaHiSeq_RNASeq

SOLiD_DNASeq_curated

IlluminaHiSeq_DNASeqC

Mixed_DNASeq_curated

IlluminaGA_RNASeq

IlluminaGA_DNASeq_Cont_automated

IlluminaGA_DNASeq

IlluminaHiSeq_WGBS

pathology_reports

IlluminaHiSeq_DNASeq_Cont_automated

Genome_Wide_SNP_6

bio

tissue_images

Mixed_DNASeq_automated

HumanMethylation27

Mixed_DNASeq_Cont_curated

samples

List of samples. Ex:c('TCGA-04-06','TCGA-61-1743-01A-01D-0649-04')

center

center name

level

'1' '2' '3'

version

List of vector with tumor/plaform/version to get old samples,

Value

A dataframe with the results of the query (lastest version of the files)

See Also

TCGAdownload for downloading the data from the search

TCGAprepare for preparing the data for the user into a Summarized experiment object, or a matrix.

Other data.functions: TCGAdownload, TCGAprepare

Examples

query <- TCGAquery(tumor = "gbm")

query <- TCGAquery(tumor = c("gbm","lgg"),
                   platform = c("HumanMethylation450","HumanMethylation27"))

query <- TCGAquery(tumor = "gbm",
                   platform = "HumanMethylation450",
                   level = "3")

query <- TCGAquery(samples = "TCGA-61-1743-01A-01D-0649-04",
                   tumor = "OV",
                   platform = "CGH-1x1M_G4447A",
                   level = 3)

# Get all LGG IlluminaHiSeq_RNASeqV2 data, but change with data version 11

query <- TCGAquery(tumor = "LGG", platform = "IlluminaHiSeq_RNASeqV2", level = "3",
                   version = list(c("IlluminaHiSeq_RNASeqV2","LGG",11)))

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