GDCquery {TCGAbiolinks} | R Documentation

## Query GDC data

### Description

Uses GDC API to search for search, it searches for both controlled and open-access data. For GDC data arguments project, data.category, data.type and workflow.type should be used For the legacy data arguments project, data.category, platform and/or file.extension should be used. Please, see the vignette for a table with the possibilities.

### Usage

    GDCquery(
      project,
      data.category,
      data.type,
      workflow.type,
      legacy = FALSE,
      access,
      platform,
      file.type,
      barcode,
      data.format,
      experimental.strategy,
      sample.type
    )

### Arguments

`project` | A list of valid project (see list with TCGAbiolinks:::getGDCprojects()$project_id)] BEATAML1.0-COHORT BEATAML1.0-CRENOLANIB CGCI-BLGSP CPTAC-2 CPTAC-3 CTSP-DLBCL1 FM-AD HCMI-CMDC MMRF-COMMPASS NCICCR-DLBCL OHSU-CNL ORGANOID-PANCREATIC TARGET-ALL-P1 TARGET-ALL-P2 TARGET-ALL-P3 TARGET-AML TARGET-CCSK TARGET-NBL TARGET-OS TARGET-RT TARGET-WT TCGA-ACC TCGA-BLCA TCGA-BRCA TCGA-CESC TCGA-CHOL TCGA-COAD TCGA-DLBC TCGA-ESCA TCGA-GBM TCGA-HNSC TCGA-KICH TCGA-KIRC TCGA-KIRP TCGA-LAML TCGA-LGG TCGA-LIHC TCGA-LUAD TCGA-LUSC TCGA-MESO TCGA-OV TCGA-PAAD TCGA-PCPG TCGA-PRAD TCGA-READ TCGA-SARC TCGA-SKCM TCGA-STAD TCGA-TGCT TCGA-THCA TCGA-THYM TCGA-UCEC TCGA-UCS TCGA-UVM VAREPOP-APOLLO
`data.category` | A valid project (see list with TCGAbiolinks:::getProjectSummary(project)) For the complete list please check the vignette. List for harmonized database: Biospecimen Clinical Copy Number Variation DNA Methylation Sequencing Reads Simple Nucleotide Variation Transcriptome Profiling List for legacy archive Biospecimen Clinical Copy number variation DNA methylation Gene expression Protein expression Raw microarray data Raw sequencing data Simple nucleotide variation
`data.type` | A data type to filter the files to download For the complete list please check the vignette.
`workflow.type` | GDC workflow type
`legacy` | Search in the legacy repository
`access` | Filter by access type. Possible values: controlled, open
`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
IlluminaHiSeq_RNASeqV2 | Mixed_DNASeq_Cont
`file.type` | To be used in the legacy database for some platforms, to define which file types to be used.
`barcode` | A list of barcodes to filter the files to download
`data.format` | Data format filter ("VCF", "TXT", "BAM","SVS","BCR XML","BCR SSF XML", "TSV", "BCR Auxiliary XML", "BCR OMF XML", "BCR Biotab", "MAF", "BCR PPS XML", "XLSX")
`experimental.strategy` | Filter to experimental strategy. Harmonized: WXS, RNA-Seq, miRNA-Seq, Genotyping Array. Legacy: WXS, RNA-Seq, miRNA-Seq, Genotyping Array, DNA-Seq, Methylation array, Protein expression array, WXS,CGH array, VALIDATION, Gene expression array,WGS, MSI-Mono-Dinucleotide Assay, miRNA expression array, Mixed strategies, AMPLICON, Exon array, Total RNA-Seq, Capillary sequencing, Bisulfite-Seq
`sample.type` | A sample type to filter the files to download

### Value

A data frame with the results and the parameters used

### Examples

    query <- GDCquery(project = "TCGA-ACC",
                      data.category = "Copy Number Variation",
                      data.type = "Copy Number Segment")
    ## Not run:
    query <- GDCquery(project = "TARGET-AML",
                      data.category = "Transcriptome Profiling",
                      data.type = "miRNA Expression Quantification",
                      workflow.type = "BCGSC miRNA Profiling",
                      barcode = c("TARGET-20-PARUDL-03A-01R","TARGET-20-PASRRB-03A-01R"))
    query <- GDCquery(project = "TARGET-AML",
                      data.category = "Transcriptome Profiling",
                      data.type = "Gene Expression Quantification",
                      workflow.type = "HTSeq - Counts",
                      barcode = c("TARGET-20-PADZCG-04A-01R","TARGET-20-PARJCR-09A-01R"))
    query <- GDCquery(project = "TCGA-ACC",
                      data.category =  "Copy Number Variation",
                      data.type = "Masked Copy Number Segment",
                      sample.type = c("Primary Tumor"))
    query.met <- GDCquery(project = c("TCGA-GBM","TCGA-LGG"),
                          legacy = TRUE,
                          data.category = "DNA methylation",
                          platform = "Illumina Human Methylation 450")
    query <- GDCquery(project = "TCGA-ACC",
                      data.category =  "Copy number variation",
                      legacy = TRUE,
                      file.type = "hg19.seg",
                      barcode = c("TCGA-OR-A5LR-01A-11D-A29H-01"))

    ## End(Not run)

[Package TCGAbiolinks version 2.20.1 Index]