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,
  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

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 2.12.5 Index]