TCGAbiolinks has provided a few functions to download and prepare data from GDC for analysis. This section starts by explaining the different downloads methods and the SummarizedExperiment object, which is the default data structure used in TCGAbiolinks, followed by some examples.

Downloading and preparing data for analysis

Data download: Methods differences

There are two methods to download GDC data using TCGAbiolinks:

client: this method creates a MANIFEST file and downloads the data using GDC Data Transfer Tool this method is more reliable but it might be slower compared to the api method.
api: this method uses the GDC Application Programming Interface (API) to download the data. This will create a MANIFEST file and the data downloaded will be compressed into a tar.gz file. If the size and the number of the files are too big this tar.gz will be too big which might have a high probability of download failure. To solve that we created the files.per.chunk argument which will split the files into small chunks, for example, if chunks.per.download is equal to 10 we will download only 10 files inside each tar.gz.

Data prepared: SummarizedExperiment object

A SummarizedExperiment object has three main matrices that can be accessed using the SummarizedExperiment package):

Sample matrix information is accessed via colData(data): stores sample information. TCGAbiolinks will add indexed clinical data and subtype information from marker TCGA papers.
Assay matrix information is accessed via assay(data): stores molecular data
Feature matrix information (gene information) is accessed via rowRanges(data): stores metadata about the features, including their genomic ranges

Summarized Experiment: annotation information

When using the function GDCprepare there is an argument called SummarizedExperiment which defines the output type a Summarized Experiment (default option) or a data frame. To create a summarized Experiment object we annotate the data with genomic positions with last patch release version of the genome available.

For legacy data (data aligned to hg19) TCGAbiolinks is using GRCh37.p13 and for harmonized data (data aligned to hg38) now it is using Gencode version 36.

Unfortunately, some of the updates changes/remove gene symbols, change coordinates, etc. Which might introduce some loss of data. For example, if the gene was removed we cannot map it anymore and that information will be lost in the SummarizedExperiment.

If you set SummarizedExperiment to FALSE, you will get the data unmodified just as they are in the files and ad your own annotation.

Also, there are no updated for DNA methylation data. But the last metadata available can be found here: http://zwdzwd.github.io/InfiniumAnnotation

simpleWarning in file.create(to[okay]) error

If you received the warning/error simpleWarning in file.create(to[okay]) try setting directory as described by some users: https://github.com/BioinformaticsFMRP/TCGAbiolinks/issues/153#issuecomment-856385673

in GDCprepare and GDCdownload

<simpleWarning in file.create(to[okay]): cannot create file ... reason 'No such file or directory'>

Arguments

`GDCdownload`

Argument	Description
query	A query for GDCquery function
token.file	Token file to download controlled data (only for method = “client”)
method	Uses the API (POST method) or gdc client tool. Options “api”, “client”. API is faster, but the data might get corrupted in the download, and it might need to be executed again
directory	Directory/Folder where the data was downloaded. Default: GDCdata
files.per.chunk	This will make the API method only download n (files.per.chunk) files at a time. This may reduce the download problems when the data size is too large. Expected a integer number (example files.per.chunk = 6)

`GDCprepare`

Argument	Description
query	A query for GDCquery function
save	Save result as RData object?
save.filename	Name of the file to be save if empty an automatic will be created
directory	Directory/Folder where the data was downloaded. Default: GDCdata
summarizedExperiment	Create a summarizedExperiment? Default TRUE (if possible)
remove.files.prepared	Remove the files read? Default: FALSE This argument will be considered only if save argument is set to true
add.gistic2.mut	If a list of genes (gene symbol) is given, columns with gistic2 results from GDAC firehose (hg19) and a column indicating if there is or not mutation in that gene (hg38) (TRUE or FALSE - use the MAF file for more information) will be added to the sample matrix in the summarized Experiment object.
mut.pipeline	If add.gistic2.mut is not NULL this field will be taken in consideration. Four separate variant calling pipelines are implemented for GDC data harmonization. Options: muse, varscan2, somaticsniper, MuTect2. For more information: https://gdc-docs.nci.nih.gov/Data/Bioinformatics_Pipelines/DNA_Seq_Variant_Calling_Pipeline/
mutant_variant_classification	List of mutant_variant_classification that will be consider a sample mutant or not. Default: “Frame_Shift_Del”, “Frame_Shift_Ins”, “Missense_Mutation”, “Nonsense_Mutation”, “Splice_Site”, “In_Frame_Del”, “In_Frame_Ins”, “Translation_Start_Site”, “Nonstop_Mutation”

Search and download data from legacy database using GDC api method

In this example we will download gene expression data from legacy database (data aligned against genome of reference hg19) using GDC api method and we will show object data and metadata.

query <- GDCquery(
    project = "TCGA-GBM",
    data.category = "Gene expression",
    data.type = "Gene expression quantification",
    platform = "Illumina HiSeq", 
    file.type  = "normalized_results",
    experimental.strategy = "RNA-Seq",
    barcode = c("TCGA-14-0736-02A-01R-2005-01", "TCGA-06-0211-02A-02R-2005-01"),
    legacy = TRUE
)
GDCdownload(
    query = query, 
    method = "api", 
    files.per.chunk = 10
)
data <- GDCprepare(query = query)

# Gene expression aligned against hg19.
datatable(
    as.data.frame(colData(data)), 
    options = list(scrollX = TRUE, keys = TRUE, pageLength = 5), 
    rownames = FALSE)

# Only first 20 rows to make render faster
datatable(
    assay(data)[1:20,], 
    options = list(scrollX = TRUE, keys = TRUE, pageLength = 5), 
    rownames = TRUE
)

rowRanges(data)

## GRanges object with 100 ranges and 3 metadata columns:
##                seqnames              ranges strand |      gene_id entrezgene
##                   <Rle>           <IRanges>  <Rle> |  <character>  <numeric>
##           A1BG    chr19   58856544-58864865      - |         A1BG          1
##            A2M    chr12     9220260-9268825      - |          A2M          2
##           NAT1     chr8   18027986-18081198      + |         NAT1          9
##           NAT2     chr8   18248755-18258728      + |         NAT2         10
##   RP11-986E7.7    chr14   95058395-95090983      + | RP11-986E7.7         12
##            ...      ...                 ...    ... .          ...        ...
##         ADORA1     chr1 203059782-203136533      + |       ADORA1        134
##        ADORA2A    chr22   24813847-24838328      + |      ADORA2A        135
##        ADORA2B    chr17   15848231-15879060      + |      ADORA2B        136
##         ADORA3     chr1 112025970-112106584      - |       ADORA3        140
##          ADPRH     chr3 119298115-119308792      + |        ADPRH        141
##                ensembl_gene_id
##                    <character>
##           A1BG ENSG00000121410
##            A2M ENSG00000175899
##           NAT1 ENSG00000171428
##           NAT2 ENSG00000156006
##   RP11-986E7.7 ENSG00000273259
##            ...             ...
##         ADORA1 ENSG00000163485
##        ADORA2A ENSG00000128271
##        ADORA2B ENSG00000170425
##         ADORA3 ENSG00000121933
##          ADPRH ENSG00000144843
##   -------
##   seqinfo: 24 sequences from an unspecified genome; no seqlengths

Search and download data for two samples from database

In this example we will download gene expression quantification from harmonized database (data aligned against genome of reference hg38). Also, it shows the object data and metadata.

# Gene expression aligned against hg38
query <- GDCquery(
    project = "TCGA-GBM",
    data.category = "Transcriptome Profiling",
    data.type = "Gene Expression Quantification", 
    workflow.type = "STAR - Counts",
    barcode = c("TCGA-14-0736-02A-01R-2005-01", "TCGA-06-0211-02A-02R-2005-01")
)
GDCdownload(query = query)
data <- GDCprepare(query = query)

datatable(
    as.data.frame(colData(data)), 
    options = list(scrollX = TRUE, keys = TRUE, pageLength = 5), 
    rownames = FALSE
)

datatable(
    assay(data)[1:20,], 
    options = list(scrollX = TRUE, keys = TRUE, pageLength = 5), 
    rownames = TRUE
)

rowRanges(data)

## GRanges object with 100 ranges and 3 metadata columns:
##                   seqnames              ranges strand | ensembl_gene_id
##                      <Rle>           <IRanges>  <Rle> |     <character>
##   ENSG00000000003     chrX 100627109-100639991      - | ENSG00000000003
##   ENSG00000000005     chrX 100584802-100599885      + | ENSG00000000005
##   ENSG00000000419    chr20   50934867-50958555      - | ENSG00000000419
##   ENSG00000000457     chr1 169849631-169894267      - | ENSG00000000457
##   ENSG00000000460     chr1 169662007-169854080      + | ENSG00000000460
##               ...      ...                 ...    ... .             ...
##   ENSG00000005421     chr7   95297676-95324707      - | ENSG00000005421
##   ENSG00000005436     chr2   75652000-75710989      - | ENSG00000005436
##   ENSG00000005448     chr2   74421678-74425755      + | ENSG00000005448
##   ENSG00000005469     chr7   87345681-87399795      + | ENSG00000005469
##   ENSG00000005471     chr7   87401697-87480435      - | ENSG00000005471
##                   external_gene_name original_ensembl_gene_id
##                          <character>              <character>
##   ENSG00000000003             TSPAN6       ENSG00000000003.13
##   ENSG00000000005               TNMD        ENSG00000000005.5
##   ENSG00000000419               DPM1       ENSG00000000419.11
##   ENSG00000000457              SCYL3       ENSG00000000457.12
##   ENSG00000000460           C1orf112       ENSG00000000460.15
##               ...                ...                      ...
##   ENSG00000005421               PON1        ENSG00000005421.7
##   ENSG00000005436              GCFC2       ENSG00000005436.12
##   ENSG00000005448              WDR54       ENSG00000005448.15
##   ENSG00000005469               CROT       ENSG00000005469.10
##   ENSG00000005471              ABCB4       ENSG00000005471.14
##   -------
##   seqinfo: 24 sequences from an unspecified genome; no seqlengths

`GDCprepare`: Outputs

This function is still under development, it is not working for all cases. See the tables below with the status. Examples of query, download, prepare can be found in this gist.

Harmonized data

Data.category	Data.type	Workflow Type	Output
Transcriptome Profiling	Gene Expression Quantification	STAR - Counts	Dataframe or SummarizedExperiment
	Isoform Expression Quantification	Not needed
	miRNA Expression Quantification	Not needed	Dataframe
Copy number variation	Copy Number Segment		Dataframe
	Masked Copy Number Segment		Dataframe
	Gene Level Copy Number		Dataframe
DNA Methylation	Methylation Beta Value		Dataframe or SummarizedExperiment
Simple Nucleotide Variation	Masked Somatic Mutation		Dataframe
Raw Sequencing Data
Biospecimen	Slide Image
Biospecimen	Biospecimen Supplement
Clinical

Legacy data

Data.category	Data.type	Platform	file.type	Status
Transcriptome Profiling
Copy number variation	-	Affymetrix SNP Array 6.0	nocnv_hg18.seg	Working
	-	Affymetrix SNP Array 6.0	hg18.seg	Working
	-	Affymetrix SNP Array 6.0	nocnv_hg19.seg	Working
	-	Affymetrix SNP Array 6.0	hg19.seg	Working
	-	Illumina HiSeq	Several	Working
Simple Nucleotide Variation	Simple somatic mutation
Raw Sequencing Data
Biospecimen
Clinical
Protein expression		MDA RPPA Core	-	Working
Gene expression	Gene expression quantification	Illumina HiSeq	normalized_results	Working
		Illumina HiSeq	results	Working
		HT_HG-U133A	-	Working
		AgilentG4502A_07_2	-	Data frame only
		AgilentG4502A_07_1	-	Data frame only
		HuEx-1_0-st-v2	FIRMA.txt	Not Preparing
			gene.txt	Not Preparing
	Isoform expression quantification
	miRNA gene quantification
	Exon junction quantification
	Exon quantification
	miRNA isoform quantification

DNA methylation		Illumina Human Methylation 450	Not used	Working
		Illumina Human Methylation 27	Not used	Working
		Illumina DNA Methylation OMA003 CPI	Not used	Working
		Illumina DNA Methylation OMA002 CPI	Not used	Working
		Illumina Hi Seq		Not working
Raw Microarray Data
Structural Rearrangement
Other

Examples

Harmonized database: data aligned against hg38

Copy Number Variation

Copy Number Segment

query <- GDCquery(
    project = "TCGA-ACC", 
    data.category = "Copy Number Variation",
    data.type = "Copy Number Segment",
    barcode = c( "TCGA-OR-A5KU-01A-11D-A29H-01", "TCGA-OR-A5JK-01A-11D-A29H-01")
)
GDCdownload(query)
data <- GDCprepare(query)

Gene Level Copy Number

query <- GDCquery(
    project = "TCGA-ACC",
    data.category = "Copy Number Variation",
    data.type = "Gene Level Copy Number",              
    access = "open"
)
GDCdownload(query)
data <- GDCprepare(query)

Allele-specific Copy Number Segment

query <- GDCquery(
    project = "TCGA-ACC",
    data.category = "Copy Number Variation",
    data.type = "Allele-specific Copy Number Segment",              
    access = "open"
)
GDCdownload(query)
data <- GDCprepare(query)

Masked Copy Number Segment

query <- GDCquery(
    project = "TCGA-ACC",
    data.category = "Copy Number Variation",
    data.type = "Masked Copy Number Segment",              
    access = "open"
)
GDCdownload(query)
data <- GDCprepare(query)

Transcriptome Profiling

Gene Expression Quantification

For more examples, please check: http://rpubs.com/tiagochst/TCGAbiolinks_RNA-seq_new_projects

# mRNA pipeline: https://gdc-docs.nci.nih.gov/Data/Bioinformatics_Pipelines/Expression_mRNA_Pipeline/
query.exp.hg38 <- GDCquery(
    project = "TCGA-GBM", 
    data.category = "Transcriptome Profiling", 
    data.type = "Gene Expression Quantification", 
    workflow.type = "STAR - Counts",
    barcode =  c("TCGA-14-0736-02A-01R-2005-01", "TCGA-06-0211-02A-02R-2005-01")
)
GDCdownload(query.exp.hg38)
expdat <- GDCprepare(
    query = query.exp.hg38,
    save = TRUE, 
    save.filename = "exp.rda"
)

miRNA Expression Quantification

library(TCGAbiolinks)
query.mirna <- GDCquery(
    project = "TARGET-AML", 
    experimental.strategy = "miRNA-Seq",
    data.category = "Transcriptome Profiling", 
    barcode = c("TARGET-20-PATDNN","TARGET-20-PAPUNR"),
    data.type = "miRNA Expression Quantification"
)
GDCdownload(query.mirna)
mirna <- GDCprepare(
    query = query.mirna,
    save = TRUE, 
    save.filename = "mirna.rda"
)

Isoform Expression Quantification

query.isoform <- GDCquery(
    project = "TARGET-AML", 
    experimental.strategy = "miRNA-Seq",
    data.category = "Transcriptome Profiling", 
    barcode = c("TARGET-20-PATDNN","TARGET-20-PAPUNR"),
    data.type = "Isoform Expression Quantification"
)
GDCdownload(query.isoform)

isoform <- GDCprepare(
    query = query.isoform,
    save = TRUE, 
    save.filename = "mirna-isoform.rda"
)

DNA methylation

Beta-values

query_met.hg38 <- GDCquery(
    project = "TCGA-BRCA", 
    data.category = "DNA Methylation", 
    data.type = "Methylation Beta Value",
    platform = "Illumina Human Methylation 27", 
    barcode = c("TCGA-B6-A0IM")
)
GDCdownload(query_met.hg38)
data.hg38 <- GDCprepare(query_met.hg38)

query_met.hg38 <- GDCquery(
    project= "TCGA-LGG", 
    data.category = "DNA Methylation", 
    data.type = "Methylation Beta Value",
    platform = "Illumina Human Methylation 450", 
    barcode = c("TCGA-HT-8111-01A-11D-2399-05","TCGA-HT-A5R5-01A-11D-A28N-05")
)
GDCdownload(query_met.hg38)
data.hg38 <- GDCprepare(query_met.hg38)


query_met.hg38 <- GDCquery(
    project= "HCMI-CMDC", 
    data.category = "DNA Methylation", 
    data.type = "Methylation Beta Value",
    platform = "Illumina Methylation Epic", 
    barcode = c("HCM-BROD-0045")
)
GDCdownload(query_met.hg38)
data.hg38 <- GDCprepare(query_met.hg38)

IDAT files

query <- GDCquery(
    project = "TCGA-BRCA",
    data.category = "DNA Methylation",
    data.type = "Masked Intensities",
    platform = "Illumina Human Methylation 27",
    legacy = FALSE
)
GDCdownload(query, files.per.chunk=10)
betas <- GDCprepare(query)

query <- GDCquery(
    project = "HCMI-CMDC",
    data.category = "DNA Methylation",
    data.type = "Masked Intensities",
    platform = "Illumina Methylation Epic",
    legacy = FALSE
)
GDCdownload(query, files.per.chunk=10)
betas <- GDCprepare(query)


query <- GDCquery(
    project = "CPTAC-3",
    data.category = "DNA Methylation",
    data.type = "Masked Intensities",
    platform = "Illumina Methylation Epic",
    legacy = FALSE
)
GDCdownload(query, files.per.chunk=10)
betas <- GDCprepare(query)

query <- GDCquery(
    project = "TCGA-BRCA",
    data.category = "DNA Methylation",
    data.type = "Masked Intensities",
    platform = "Illumina Methylation Epic",
    legacy = FALSE
)
GDCdownload(query, files.per.chunk=10)
betas <- GDCprepare(query)

Proteome Profiling

Protein Expression Quantification

query.rppa <- GDCquery(
    project = "TCGA-ESCA", 
    data.category = "Proteome Profiling",
    data.type = "Protein Expression Quantification"
)
GDCdownload(query.rppa) 
rppa <- GDCprepare(query.rppa)

Clinical

query <- GDCquery(
    project = "TCGA-COAD",
    data.category = "Clinical",
    data.type = "Clinical Supplement",
    data.format = "BCR XML",
    barcode = "TCGA-A6-5664"
)
GDCdownload(query)
drug <- GDCprepare_clinic(query,"drug")

query <- GDCquery(
    project = "TCGA-COAD",
    data.category = "Clinical",
    data.type = "Clinical Supplement",
    data.format = "BCR OMF XML",
    barcode = "TCGA-AD-6964"
)
GDCdownload(query)


query <- GDCquery(
    project = "TCGA-ACC", 
    data.category = "Clinical",
    data.type = "Clinical Supplement", 
    data.format = "BCR Biotab"
)
GDCdownload(query)
clinical.BCRtab.all <- GDCprepare(query)
names(clinical.BCRtab.all)

query <- GDCquery(
    project = "TCGA-ACC", 
    data.category = "Clinical",
    data.type = "Clinical Supplement", 
    data.format = "BCR Biotab",
    file.type = "radiation"
)
GDCdownload(query)
clinical.BCRtab.radiation <- GDCprepare(query)

Simple Nucleotide Variation

Masked Somatic Mutation

For more information please check: https://docs.gdc.cancer.gov/Data/Bioinformatics_Pipelines/DNA_Seq_Variant_Calling_Pipeline/

query <- GDCquery(
    project = "TCGA-HNSC", 
    data.category = "Simple Nucleotide Variation",
    data.type = "Masked Somatic Mutation",
    access = "open"
)
GDCdownload(query)
maf <- GDCprepare(query)

Single cell

GDC Single Cell RNA-Seq information: https://docs.gdc.cancer.gov/Data/Bioinformatics_Pipelines/Expression_mRNA_Pipeline/#scrna-seq-pipeline-single-nuclei

query.sc.analysis <- GDCquery(
    project = "CPTAC-3", 
    data.category = "Transcriptome Profiling",
    legacy = FALSE,
    access = "open",
    data.type = "Single Cell Analysis",
    data.format =  "TSV"
)  
GDCdownload(query.sc.analysis)
Single.Cell.Analysis.list <- GDCprepare(query.sc.analysis)

query.raw.counts <- GDCquery(
    project = "CPTAC-3", 
    data.category = "Transcriptome Profiling",
    legacy = FALSE,
    access = "open",
    data.type = "Gene Expression Quantification",
    barcode = c("CPT0167860015","CPT0206880004"),
    workflow.type = "CellRanger - 10x Raw Counts"
)  
GDCdownload(query.raw.counts)
raw.counts.list <- GDCprepare(query.raw.counts)

query.filtered.counts <- GDCquery(
    project = "CPTAC-3", 
    data.category = "Transcriptome Profiling",
    legacy = FALSE,
    access = "open",
    data.type = "Gene Expression Quantification",
    barcode = c("CPT0167860015","CPT0206880004"),
    workflow.type = "CellRanger - 10x Filtered Counts"
)  
GDCdownload(query.filtered.counts)
filtered.counts.list <- GDCprepare(query.filtered.counts)

query.sc.dea <- GDCquery(
    project = "CPTAC-3", 
    data.category = "Transcriptome Profiling",
    legacy = FALSE,
    access = "open",
    data.type = "Differential Gene Expression",
    barcode = c("CPT0167860015","CPT0206880004"),
    workflow.type = "Seurat - 10x Chromium"
)  
GDCdownload(query.sc.dea)
sc.dea.list <- GDCprepare(query.sc.dea)

Legacy archive: data aligned against hg19

DNA methylation: Get all TCGA IDAT files

#-------------------------------------------------------
# Example to idat files from TCGA projects
#-------------------------------------------------------
projects <- TCGAbiolinks:::getGDCprojects()$project_id
projects <- projects[grepl('^TCGA',projects,perl=T)]
match.file.cases.all <- NULL
for(proj in projects){
    print(proj)
    query <- GDCquery(
        project = proj,
        data.category = "Raw microarray data",
        data.type = "Raw intensities", 
        experimental.strategy = "Methylation array", 
        legacy = TRUE,
        file.type = ".idat",
        platform = "Illumina Human Methylation 450"
    )
    match.file.cases <- getResults(query,cols=c("cases","file_name"))
    match.file.cases$project <- proj
    match.file.cases.all <- rbind(match.file.cases.all,match.file.cases)
    tryCatch(
        GDCdownload(query, method = "api", files.per.chunk = 20),
        error = function(e) GDCdownload(query, method = "client")
    )
}
# This will create a map between idat file name, cases (barcode) and project
readr::write_tsv(match.file.cases.all, path =  "idat_filename_case.txt")
# code to move all files to local folder
for(file in dir(".",pattern = ".idat", recursive = T)){
    TCGAbiolinks::move(file,basename(file))
}

DNA methylation

query_meth.hg19 <- GDCquery(
    project= "TCGA-LGG", 
    data.category = "DNA methylation", 
    platform = "Illumina Human Methylation 450", 
    barcode = c("TCGA-HT-8111-01A-11D-2399-05","TCGA-HT-A5R5-01A-11D-A28N-05"), 
    legacy = TRUE
)
GDCdownload(query_meth.hg19)
data.hg19 <- GDCprepare(query_meth.hg19)

Protein expression

query <- GDCquery(
    project = "TCGA-GBM",
    data.category = "Protein expression",
    legacy = TRUE, 
    barcode = c("TCGA-OX-A56R-01A-21-A44T-20","TCGA-08-0357-01A-21-1898-20")
)
GDCdownload(query)
data <- GDCprepare(
    query, save = TRUE, 
    save.filename = "gbmProteinExpression.rda",
    remove.files.prepared = TRUE
)

Gene expression

# Aligned against Hg19
query.exp.hg19 <- GDCquery(
    project = "TCGA-GBM",
    data.category = "Gene expression",
    data.type = "Gene expression quantification",
    platform = "Illumina HiSeq", 
    file.type  = "normalized_results",
    experimental.strategy = "RNA-Seq",
    barcode = c("TCGA-14-0736-02A-01R-2005-01", "TCGA-06-0211-02A-02R-2005-01"),
    legacy = TRUE
)
GDCdownload(query.exp.hg19)
data <- GDCprepare(query.exp.hg19)

TCGAbiolinks: Downloading and preparing files for analysis

20 September 2022

Downloading and preparing data for analysis

Arguments

`GDCdownload`

`GDCprepare`

Search and download data from legacy database using GDC api method

Search and download data for two samples from database

`GDCprepare`: Outputs

Harmonized data

Legacy data

Examples

Harmonized database: data aligned against hg38

Copy Number Variation

Copy Number Segment

Gene Level Copy Number

Allele-specific Copy Number Segment

Masked Copy Number Segment

Transcriptome Profiling

Gene Expression Quantification

miRNA Expression Quantification

Isoform Expression Quantification

DNA methylation

Beta-values

IDAT files

Proteome Profiling

Protein Expression Quantification

Clinical

Simple Nucleotide Variation

Masked Somatic Mutation

Single cell

Legacy archive: data aligned against hg19

DNA methylation: Get all TCGA IDAT files

DNA methylation

Protein expression

Gene expression

TCGAbiolinks: Downloading and preparing files for analysis

20 September 2022

Downloading and preparing data for analysis

Arguments

GDCdownload

GDCprepare

Search and download data from legacy database using GDC api method

Search and download data for two samples from database

GDCprepare: Outputs

Harmonized data

Legacy data

Examples

Harmonized database: data aligned against hg38

Copy Number Variation

Copy Number Segment

Gene Level Copy Number

Allele-specific Copy Number Segment

Masked Copy Number Segment

Transcriptome Profiling

Gene Expression Quantification

miRNA Expression Quantification

Isoform Expression Quantification

DNA methylation

Beta-values

IDAT files

Proteome Profiling

Protein Expression Quantification

Clinical

Simple Nucleotide Variation

Masked Somatic Mutation

Single cell

Legacy archive: data aligned against hg19

DNA methylation: Get all TCGA IDAT files

DNA methylation

Protein expression

Gene expression

`GDCdownload`

`GDCprepare`

`GDCprepare`: Outputs