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TCGAbiolinks_DNA_methylation_data.md

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Processing HARMONIZED DNA methylation data

NOTE: Needs updates!!!

Pipeline for downloading HARMONIZED DNA methylation data from TCGA and TARGET projects using TCGAbiolinks R package. The script outputs matrix with DNA methylation data for user-defined tissue types along with associated clinical information.

The TCGA genomic data harmonization is here and the the DNA methylation liftover pipeline is described here.

Arguments

  1. Local workspace. This is the directory to which the data will be downloaded and stored.

  2. Project ID. Available TCGA/TARGET project IDs are:

    Project ID Name
    TCGA-SARC Sarcoma
    TCGA-MESO Mesothelioma
    TCGA-READ Rectum Adenocarcinoma
    TCGA-KIRP Kidney Renal Papillary Cell Carcinoma
    TARGET-NBL Neuroblastoma
    TCGA-PAAD Pancreatic Adenocarcinoma
    TCGA-GBM Glioblastoma Multiforme
    TCGA-ACC Adrenocortical Carcinoma
    TARGET-OS Osteosarcoma
    TCGA-CESC Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma
    TARGET-RT Rhabdoid Tumour
    TCGA-BRCA Breast Invasive Carcinoma
    TCGA-ESCA Esophageal Carcinoma
    TCGA-DLBC Lymphoid Neoplasm Diffuse Large B-cell Lymphoma
    TCGA-KICH Kidney Chromophobe
    TCGA-KIRC Kidney Renal Clear Cell Carcinoma
    TCGA-UVM Uveal Melanoma
    TARGET-AML Acute Myeloid Leukaemia
    TCGA-LAML Acute Myeloid Leukaemia
    TCGA-SKCM Skin Cutaneous Melanoma
    TCGA-PCPG Pheochromocytoma and Paraganglioma
    TCGA-COAD Colon Adenocarcinoma
    TCGA-UCS Uterine Carcinosarcoma
    TCGA-LUSC Lung Squamous Cell Carcinoma
    TCGA-LGG Brain Lower Grade Glioma
    TCGA-HNSC Head and Neck Squamous Cell Carcinoma
    TCGA-TGCT Testicular Germ Cell Tumours
    TARGET-CCSK Clear Cell Sarcoma of the Kidney
    TCGA-THCA Thyroid Carcinoma
    TCGA-LIHC Liver Hepatocellular Carcinoma
    TCGA-BLCA Bladder Urothelial Carcinoma
    TCGA-UCEC Uterine Corpus Endometrial Carcinoma
    TARGET-WT High-Risk Wilms Tumour
    TCGA-PRAD Prostate Adenocarcinoma
    TCGA-OV Ovarian Serous Cystadenocarcinoma
    TCGA-THYM Thymoma
    TCGA-CHOL Cholangiocarcinoma
    TCGA-STAD Stomach Adenocarcinoma
    TCGA-LUAD Lung Adenocarcinoma

  1. Tissue code. Tissue types to be considered for download. Each tissue type is expected to be separated by comma. Type 'all' for all listed tissue types to be considered for download. Available options are:

    Tissue code Letter code Definition
    1 TP Primary solid Tumour
    2 TR Recurrent Solid Tumour
    3 TB Primary Blood Derived Cancer - Peripheral Blood
    4 TRBM Recurrent Blood Derived Cancer - Bone Marrow
    5 TAP Additional - New Primary
    6 TM Metastatic
    7 TAM Additional Metastatic
    8 THOC Human Tumour Original Cells
    9 TBM Primary Blood Derived Cancer - Bone Marrow
    10 NB Blood Derived Normal
    11 NT Solid Tissue Normal
    12 NBC Buccal Cell Normal
    13 NEBV EBV Immortalised Normal
    14 NBM Bone Marrow Normal
    20 CELLC Control Analyte
    40 TRB Recurrent Blood Derived Cancer - Peripheral Blood
    50 CELL Cell Lines
    60 XP Primary Xenograft Tissue
    61 XCL Cell Line Derived Xenograft Tissue
    All --- All available tissue types

  1. Platform. Available data may have been produced using one of two platforms:

    Platform Full name
    HM27 Illumina Infinium Human Methylation 27
    HM450 Illumina Infinium Human HumanMethylation 450

Command line use example

      R --file=./TCGAbiolinks_DNA_methylation_data.R --args "TCGA_data/TCGA-PAAD" "TCGA-PAAD" "1,11" "HM450"

Output data directory structure

TCGA_data
|
|____TCGA-PAAD
  |
  |____DNA_methylation
    |
    |____HM450
      |____HM450.txt
      |____HM450_boxplot.pdf
      |____HM450_clinical_info.txt
      |____HM450_samples.txt
      |____gdc-client
      |____gdc-client_v1.1.0_OSX_x64.zip
      |____gdc_manifest.txt
      |____R_parameters.txt
      |____GDCdata
        |
        |____TCGA-PAAD
          |
          |____harmonized
            |
            |____DNA_Methylation
            | |
            | |____Methylation_Beta_Value
            |   |____…
            |   |____…
            |
            |____Clinical
              |
              |____Clinical_Supplement
                |____…
                |____…

Files description

File Description
HM450.txt DNA methylation (Beta values) matrix
HM450_boxplot.pdf Box plot of DNA methylation data (Beta values) per sample
HM450_clinical_info.txt Samples and associated clinical annotation
R_parameters.txt User-defined parameters used for the script execution
DNA_Methylation Folder with compressed 'txt' files containing DNA methylation (Beta) values for each sample
Clinical_Supplement Folder with 'xml' files including clinical information for each sample

Note

Make sure that R version >= 3.3 is installed. For older versions the TCGAbiolinks uses different functions starting with "TCGA" rather than "GDC" since the data were moved from DCC server to NCI Genomic Data Commons (GDC). Make sure that the newest TCGAbiolinks package is installed.

devtools::install_github(repo = "BioinformaticsFMRP/TCGAbiolinks")