TCGAbiolinks has provided a few functions to search GDC database. This section starts by explaining the different GDC sources (Harmonized and Legacy Archive), followed by some examples how to access them.


Useful information

Different sources: Legacy vs Harmonized

There are two available sources to download GDC data using TCGAbiolinks:

  • GDC Legacy Archive : provides access to an unmodified copy of data that was previously stored in CGHub and in the TCGA Data Portal hosted by the TCGA Data Coordinating Center (DCC), in which uses as references GRCh37 (hg19) and GRCh36 (hg18).
  • GDC harmonized database: data available was harmonized against GRCh38 (hg38) using GDC Bioinformatics Pipelines which provides methods to the standardization of biospecimen and clinical data.
Understanding the barcode

A TCGA barcode is composed of a collection of identifiers. Each specifically identifies a TCGA data element. Refer to the following figure for an illustration of how metadata identifiers comprise a barcode. An aliquot barcode contains the highest number of identifiers.

Example:

  • Aliquot barcode: TCGA-G4-6317-02A-11D-2064-05
  • Participant: TCGA-G4-6317
  • Sample: TCGA-G4-6317-02

For more information check TCGA wiki

Searching arguments

You can easily search GDC data using the GDCquery function.

Using a summary of filters as used in the TCGA portal, the function works with the following arguments:

?project A list of valid project (see table below)]
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

project options

The options for the field project are below:

sample.type options

The options for the field sample.type are below:

The other fields (data.category, data.type, workflow.type, platform, file.type) can be found below. Please, note that these tables are still incomplete.

Harmonized data options (legacy = FALSE)

## Parsed with column specification:
## cols(
##   Data.category = col_character(),
##   Data.type = col_character(),
##   `Workflow Type` = col_character(),
##   Platform = col_character()
## )

Legacy archive data options (legacy = TRUE)

## Parsed with column specification:
## cols(
##   Data.category = col_character(),
##   Data.type = col_character(),
##   Platform = col_character(),
##   file.type = col_character()
## )

Harmonized database examples

DNA methylation data: Recurrent tumor samples

In this example we will access the harmonized database (legacy = FALSE) and search for all DNA methylation data for recurrent glioblastoma multiform (GBM) and low grade gliomas (LGG) samples.

Samples with DNA methylation and gene expression data

In this example we will access the harmonized database (legacy = FALSE) and search for all patients with DNA methylation (platform HumanMethylation450k) and gene expression data for Colon Adenocarcinoma tumor (TCGA-COAD).

Raw Sequencing Data: Finding the match between file names and barcode for Controlled data.

This exmaple shows how the user can search for breast cancer Raw Sequencing Data (“Controlled”) and verify the name of the files and the barcodes associated with it.

Legacy archive examples

DNA methylation

Array-based assays

This example shows how the user can search for glioblastoma multiform (GBM) and low grade gliomas (LGG) DNA methylation data for platform Illumina Human Methylation 450 and Illumina Human Methylation 27.

Gene expression

This exmaple shows how the user can search for glioblastoma multiform (GBM) gene expression data with the normalized results for expression of a gene. For more information check rnaseqV2 TCGA wiki

Get Manifest file

If you want to get the manifest file from the query object you can use the function getManifest. If you set save to TRUEm a txt file that can be used with GDC-client Data transfer tool (DTT) or with its GUI version ddt-ui will be created.

##                                      id
## 40 217d72e9-4d6f-409d-911c-0a70b17a0adc
## 97 973ce0ac-f613-4b99-b2ab-3e2d5548f05f
##                                                                              filename
## 40 unc.edu.b469eb7c-723f-4870-b4e4-ebfaae7a118b.1536566.rsem.genes.normalized_results
## 97 unc.edu.152afe8c-f67c-4d7c-93ac-e1b7edd56c54.1544649.rsem.genes.normalized_results
##                                 md5   size state
## 40 beda9f89f08fc6a892a72e8b704fdbd9 437283  live
## 97 84478e78d95e1155019ccb7e0e0fea2f 436272  live

ATAC-seq data

For the moment, ATAC-seq data is available at the GDC publication page.

The list of file available is below:

You can use the function GDCquery_ATAC_seq filter the manifest table and use GDCdownload to save the data locally.

Summary of available files per patient

Retrieve the numner of files under each data_category + data_type + experimental_strategy + platform. Almost like https://portal.gdc.cancer.gov/exploration