GDCquery: Query GDC data

In TCGAbiolinks: TCGAbiolinks: An R/Bioconductor package for integrative analysis with 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)

TCGAbiolinks documentation built on Nov. 8, 2020, 5:37 p.m.