TARGET-NBL
Query
query <- GDCquery(
project = "TARGET-NBL",
data.category = "Transcriptome Profiling",
data.type = "Gene Expression Quantification",
workflow.type = "STAR - Counts",
sample.type = "Primary Tumor"
)Download
GDCdownload(query,files.per.chunk = 100)Prepare
data <- GDCprepare(query)##
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|====================================================|100% Completed after 11 s## Starting to add information to samples## Adding description to TARGET samples## => Add clinical information to samples## Available assays in SummarizedExperiment :
## => unstranded
## => stranded_first
## => stranded_second
## => tpm_unstrand
## => fpkm_unstrand
## => fpkm_uq_unstranddata## class: RangedSummarizedExperiment
## dim: 60660 149
## metadata(1): data_release
## assays(6): unstranded stranded_first ... fpkm_unstrand fpkm_uq_unstrand
## rownames(60660): ENSG00000000003.15 ENSG00000000005.6 ...
## ENSG00000288674.1 ENSG00000288675.1
## rowData names(10): source type ... hgnc_id havana_gene
## colnames(149): TARGET-30-PASMNT-01A-01R TARGET-30-PARSBI-01A-01R ...
## TARGET-30-PARNNC-01A-01R TARGET-30-PAKZRH-01A-01R
## colData names(46): nucleic.acid.code tumor.code ... releasable releasedSession information
devtools::session_info()## ─ Session info ───────────────────────────────────────────────────────────────
## setting value
## version R version 4.2.0 (2022-04-22)
## os macOS Big Sur/Monterey 10.16
## system x86_64, darwin17.0
## ui X11
## language (EN)
## collate en_US.UTF-8
## ctype en_US.UTF-8
## tz America/Sao_Paulo
## date 2022-07-04
## pandoc 2.17.1.1 @ /Applications/RStudio.app/Contents/MacOS/quarto/bin/ (via rmarkdown)
##
## ─ Packages ───────────────────────────────────────────────────────────────────
## ! package * version date (UTC) lib source
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## Biobase 2.56.0 2022-04-26 [1] Bioconductor
## BiocFileCache 2.4.0 2022-04-26 [1] Bioconductor
## BiocGenerics 0.42.0 2022-04-26 [1] Bioconductor
## biomaRt 2.52.0 2022-04-26 [1] Bioconductor
## Biostrings 2.64.0 2022-04-26 [1] Bioconductor
## bit 4.0.4 2020-08-04 [1] CRAN (R 4.2.0)
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## blob 1.2.3 2022-04-10 [1] CRAN (R 4.2.0)
## brio 1.1.3 2021-11-30 [1] CRAN (R 4.2.0)
## bslib 0.3.1 2021-10-06 [1] CRAN (R 4.2.0)
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## colorspace 2.0-3 2022-02-21 [1] CRAN (R 4.2.0)
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## curl 4.3.2 2021-06-23 [1] CRAN (R 4.2.0)
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## htmltools 0.5.2 2021-08-25 [1] CRAN (R 4.2.0)
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## IRanges 2.30.0 2022-04-26 [1] Bioconductor
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## lifecycle 1.0.1 2021-09-24 [1] CRAN (R 4.2.0)
## magrittr 2.0.3 2022-03-30 [1] CRAN (R 4.2.0)
## Matrix 1.4-1 2022-03-23 [1] CRAN (R 4.2.0)
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## pkgconfig 2.0.3 2019-09-22 [1] CRAN (R 4.2.0)
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## prettydoc 0.4.1 2021-01-10 [1] CRAN (R 4.2.0)
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## R.methodsS3 1.8.2 2022-06-13 [1] CRAN (R 4.2.0)
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## R.utils 2.12.0 2022-06-28 [1] CRAN (R 4.2.0)
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## remotes 2.4.2 2021-11-30 [1] CRAN (R 4.2.0)
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## rmarkdown 2.14 2022-04-25 [1] CRAN (R 4.2.0)
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## rstudioapi 0.13 2020-11-12 [1] CRAN (R 4.2.0)
## rvest 1.0.2 2021-10-16 [1] CRAN (R 4.2.0)
## S4Vectors 0.34.0 2022-04-26 [1] Bioconductor
## sass 0.4.1 2022-03-23 [1] CRAN (R 4.2.0)
## scales 1.2.0 2022-04-13 [1] CRAN (R 4.2.0)
## sessioninfo 1.2.2 2021-12-06 [1] CRAN (R 4.2.0)
## stringi 1.7.6 2021-11-29 [1] CRAN (R 4.2.0)
## stringr 1.4.0 2019-02-10 [1] CRAN (R 4.2.0)
## SummarizedExperiment 1.26.1 2022-05-01 [1] Bioconductor
## VP TCGAbiolinks * 2.25.2 2022-06-16 [?] Bioconductor (on disk 2.24.3)
## TCGAbiolinksGUI.data 1.16.0 2022-04-28 [1] Bioconductor
## testthat * 3.1.4 2022-04-26 [1] CRAN (R 4.2.0)
## tibble 3.1.7 2022-05-03 [1] CRAN (R 4.2.0)
## tidyr 1.2.0 2022-02-01 [1] CRAN (R 4.2.0)
## tidyselect 1.1.2 2022-02-21 [1] CRAN (R 4.2.0)
## tzdb 0.3.0 2022-03-28 [1] CRAN (R 4.2.0)
## usethis 2.1.6 2022-05-25 [1] CRAN (R 4.2.0)
## utf8 1.2.2 2021-07-24 [1] CRAN (R 4.2.0)
## vctrs 0.4.1 2022-04-13 [1] CRAN (R 4.2.0)
## withr 2.5.0 2022-03-03 [1] CRAN (R 4.2.0)
## xfun 0.31 2022-05-10 [1] CRAN (R 4.2.0)
## XML 3.99-0.10 2022-06-09 [1] CRAN (R 4.2.0)
## xml2 1.3.3 2021-11-30 [1] CRAN (R 4.2.0)
## XVector 0.36.0 2022-04-26 [1] Bioconductor
## yaml 2.3.5 2022-02-21 [1] CRAN (R 4.2.0)
## zlibbioc 1.42.0 2022-04-26 [1] Bioconductor
##
## [1] /Library/Frameworks/R.framework/Versions/4.2/Resources/library
##
## V ── Loaded and on-disk version mismatch.
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##
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