GDCquery {TCGAbiolinks} | R Documentation |
Uses GDC API to search for search, it searches for both controlled and open-acess 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.
GDCquery(project, data.category, data.type, workflow.type, legacy = FALSE, access, platform, file.type, barcode, data.format, experimental.strategy, sample.type)
project |
A list of valid project (see list with TCGAbiolinks:::getGDCprojects()$project_id)] | ||||||||||||||||||||||||||||||||||||||||||||||
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:
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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 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 |
A data frame with the results and the parameters used
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 solid 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)