GDCquery {TCGAbiolinks} | R Documentation

## Query GDC data

### Description

Uses GDC API to search for search, it searches for both controlled and open-acess 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)]
`data.category` | A valid project (see list with TCGAbiolinks:::getProjectSummary(project))
`data.type` | A data type to filter the files to download
`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 stratey. 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 solid 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 2.14.0 Index]