Description Usage Arguments Value Examples
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.
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project |
A list of valid project (see list with TCGAbiolinks:::getGDCprojects()$project_id)]
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data.category |
A valid project (see list with TCGAbiolinks:::getProjectSummary(project)) For the complete list please check the vignette. List for harmonized database:
List for legacy archive
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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:
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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 |
A data frame with the results and the parameters used
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 | 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)
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